Reticulate Evolution in Eukaryotes: Origin and Evolution of The

bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license.

Reticulate evolution in eukaryotes: origin and evolution of the

nitrate assimilation pathway

Eduard Ocaña-Pallarès1*, Sebastián R. Najle1, 2; Claudio Scazzocchio3,4; Iñaki Ruiz-Trillo1, 5, 6*

5 1. Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la

Barceloneta 37-49, Barcelona 08003, Catalonia, Spain

2. Instituto de Biología Molecular y Celular de Rosario (IBR) CONICET and Facultad de Ciencias

Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n,

Rosario S2000FHQ, Argentina

10 3. Department of Microbiology, Imperial College, London, United Kingdom

4. Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France

5. Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca

de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Catalonia, Spain

6. ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Catalonia, Spain

* To whom correspondence may be addressed: [email protected], [email protected]

Abstract

Genes and genomes can evolve through interchanging genetic material, this leading to reticular

evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular

20 of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with

taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate

assimilation pathway is an ideal object of investigation, as previous results revealed a patchy

distribution and suggested one crucial HGT event. We studied the evolution of this pathway through

both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening

25 shows this pathway to be present in more lineages than previously proposed and that nitrate

assimilation is restricted to autotrophs and to distinct osmotrophic groups. Our phylogenies show a

pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least

seven well-supported transfers between eukaryotes. Our results, based on a larger dataset, differ

from the previously proposed transfer of a nitrate assimilation cluster from Oomycota

30 (Stramenopiles) to Dikarya (Fungi, Opisthokonta). We propose a complex HGT path involving at

least two cluster transfers between Stramenopiles and Opisthokonta. We also found that gene fusion

played an essential role in this evolutionary history, underlying the origin of the canonical eukaryotic

nitrate reductase, and of a novel nitrate reductase in Ichthyosporea (Opisthokonta). We show that

the ichthyosporean pathway, including this novel nitrate reductase, is physiologically active and

35 transcriptionally co-regulated, responding to different nitrogen sources; similarly to distant

eukaryotes with independent HGT-acquisitions of the pathway. This indicates that this pattern of

transcriptional control evolved convergently in eukaryotes, favoring the proper integration of the

pathway in the metabolic landscape. Our results highlight the importance of reticulate evolution in

eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history

40 of the nitrate assimilation pathway.

Introduction 45 One of the most significant advances in evolution was the realization that lineages, either genes or

genomes, can also evolve through interchanging genetic material, this leading to reticulate

evolutionary patterns [1,2]. Reticulate evolution, and in particular horizontal gene transfer (HGT), is

widely accepted as an important mechanism in prokaryotes [3]. However, its occurrence is still

50 subject to controversy in eukaryotes, and its prevalence and mechanistic basis are active areas of

study [4,5]. The finding of homologous genes in distantly related lineages may suggest the

occurrence of HGT events [6]. However, taxonomically-patchy distributed genes can also be the

result of secondary losses. Hence, the most accurate methodology for HGT detection consists of

finding topological incongruences between the reconstructed phylogenetic trees and the species

55 phylogeny [7].

Adaptation to new environments requires metabolic remodeling, and HGT of metabolic genes

between prokaryotes occurs at a higher rate than that of informational genes [8]; which may facilitate

the recipients’ rapid adaptation [9]. Numerous metabolic pathways in eukaryotes are of bacterial

60 origin [6], transferred from endosymbionts [10]; and many proposed HGTs between eukaryotes also

involve metabolic genes [11–13]. Hence, patchily distributed metabolic pathways make good

candidate subjects for investigation into possible events of HGT in eukaryotes.

The eukaryotic nitrate assimilation pathway is strikingly patchily distributed [14]. The ability to use

65 nitrate as a nitrogen source is not essential, but valuable in nitrate-rich environments [15,16]. In order

to reduce nitrate to ammonium, a specific pathway is required, involving minimally a nitrate

transporter, a nitrate reductase and a nitrite reductase (Nitrate Assimilation Proteins, NAPs) [17]. In

eukaryotes, NAPs were characterized in plants and fungi and were later identified in other

eukaryotes, including green and red alga, diatoms and Oomycota [14,18]. A study published a

70 decade ago proposed that the nitrate assimilation pathway characteristic of many fungal species

originated in a stramenopiles lineage leading to Oomycota, and then was transferred as a cluster

from Oomycota to the root of Dikarya (Fungi). The authors also hypothesized that the acquisition of

this metabolic pathway might have been an important innovation for the colonization of dry land by

this fungal group [14]. However, the absence of genomic data from many eukaryotic groups left

75 uncertainty surrounding this proposed HGT event as well as the degree to which HGT influenced

the evolutionary history of this pathway in eukaryotes. We therefore performed an extensive survey

of NAPs and NAP clusters in order to understand the origins and the evolution of the eukaryotic

nitrate assimilation pathway.

80 Our updated taxon sampling extends the presence of this ecologically-relevant pathway to many

previously unsampled lineages, showing a patchy distribution that overlaps with the distribution of

autotrophy and osmotrophy in the eukaryotic tree. The reconstructed history indicates a pervasive

role of HGT underlying this patchy distribution, with three independent bacterial transfers contributing

to the origins of the pathway and at least seven well-supported transfers of NAPs and NAP clusters

85 between eukaryotes. Our results do not agree with the proposed origin and transfer of a NAP cluster

from Oomycota to dikaryotic fungi. Instead, we propose that the NAP cluster was assembled in a

common ancestor of Alveolata and Stramenopiles, with Fungi vertically inheriting it from a

stramenopiles transfer to an ancestral opisthokont. We also propose a horizontal origin of the

Oomycota NAP cluster from Ichthyosporea, a group of unicellular relatives of animals. Gene fusion

90 was also crucial in the evolution of this pathway, underlying the origin of the canonical eukaryotic

nitrate reductase; as well as of a nitrate reductase of chimeric origins found in the NAP clusters of

two ichthyosporeans. Finally, we demonstrate that this cluster is functional in the ichthyosporean

Sphaeroforma arctica, with NAPs showing a strong co-regulation in response to environmental

nitrogen sources. The similarities of this transcriptional control with that shown for many lineages

95 with distinct horizontal acquisitions of the pathway indicate that this regulatory response has

convergently evolved multiple times in eukaryotes.

Results

NAP genes in eukaryotes

100 The minimal metabolic pathway required to incorporate nitrate into the cell and reduce it into

ammonium includes a nitrate transporter, a nitrate reductase and a nitrite reductase (Fig 1) [18]. The

nitrate transporter NRT2 and the nitrate reductase EUKNR are involved in the first two steps of the

pathway in all the eukaryotes where this metabolism has been studied. For the third and last step of

the pathway, two nitrite reductases have been characterized in eukaryotes: a chloroplastic

105 ferredoxin-dependent enzyme (Fd-NIR, characterized in land plants and green algae); and a

cytoplasmic NAD(P)H dependent cytosolic enzyme (NAD[P]H-NIR, characterized in fungi).

We screened NAP genes in a taxon sampling designed to cover the broadest possible eukaryotic

diversity (Fig 2). Among the 60 taxa with at least one NAP gene detected, 47 have the complete

110 pathway (i.e. the transporter, the nitrate reductase and one of the two nitrite reductases; see

Supplementary Fig 1 and Supplementary Table 1. All supplementary tables are in Supplementary

File 2; supplementary files are accessible in https://figshare.com/s/d11b23d7928009e2d508). The

distribution of NAP genes across eukaryotes is highly correlated, as it would be expected for genes

involved in the same pathway (Supplementary Fig 2A). However, considering only taxa with at least

115 one NAP gene, the two nitrite reductases, NAD(P)H-nir and Fd-nir, show an almost completely anti-

correlated distribution (Supplementary Fig 2B). Fd-nir is restricted to autotrophic lineages (including

facultative autotrophs), as expected for a chloroplastic enzyme [19]. In contrast, NAD(P)H-nir is

mostly distributed along heterotrophs, except for the myzozoans Symbiodinium minutum and Vitrella

brassicaformis, in which the Fd-nir is absent; and four Ochrophyta species, in which both nitrite

120 reductases are present.

The widespread and patchy distribution of NAP genes is correlated with the distribution of different

nutrient acquisition strategies within the eukaryotic tree (Supplementary Fig 2C). We found NAP

genes in all the sampled autotrophs (see green circles in Fig 2). This includes taxa from groups

125 whose plastid originated from a cyanobacterial endosymbiont (primary plastids): Glaucophyta,

Rhodophyta and Chloroplastida; as well as algal groups whose plastid originated from an eukaryotic

endosymbiont (complex plastids): Haptophyta, Cryptophyta, Chlorarachniophyta, S. minutum, V.

brassicaformis and Ochrophyta [20]. Among heterotrophs, we found the complete pathway in Fungi

and Oomycota, as reported in previous studies, but also in Teretosporea and Labyrinthulea. These

130 groups are phylogenetically distant but share many analogous cellular and ecological features

related to their proposed convergent evolution towards an osmotrophic lifestyle [21] (Fungal-like

osmotrophs, see brown circles in Fig 2). We did not find the entire nitrate assimilation pathway in

any of the phagotrophic lineages sampled (Supplementary Fig 2C).

135 The distinct origins of NAP genes in eukaryotes

Previous studies proposed a bacterial origin for the transporter and the two nitrite reductases [14].

However, which particular bacterial group(s) were the possible donors of these three NAP genes

was not determined. We investigated the origin of Fd-nir, NAD(P)H-nir and nrt2 in eukaryotes using

a comprehensive and taxonomically representative prokaryotic dataset.

140

The bacterial donors of Fd-nir, NAD(P)H-nir and nrt2

The reconstructed phylogenies of these three NAPs with prokaryotic homologs show in all cases a

well-supported monophyletic clade that includes eukaryotic sequences branching distantly to

archaeal ones (Fig 3). These suggest that each NAP descends from a single eukaryotic acquisition,

145 and also that they were not vertically inherited from Archaea, but horizontally transferred from

Bacteria to eukaryotes.

Our phylogeny supports that the eukaryotic nitrite reductase Fd-NIR descends from Cyanobacteria,

as was previously suggested based on sequence-similarity analyses [22] (100% UFboot; Fig 3 and

150 Supplementary Fig 3). Because of its cyanobacterial origin and given that Fd-NIR activity has been

located in the chloroplast, it is tempting to propose that Fd-nir was transferred to eukaryotes from

the cyanobacterial endosymbiont from which all the primary plastids originated. However, not all the

proteins of plastidic activity originated from this organelle [23], so it remains unclear whether Fd-nir

originated from the endosymbiont or not. If Fd-nir is of plastidic origin, we would then expect a similar

155 phylogenetic position of the eukaryotic Fd-NIR in relation to Cyanobacteria than in the phylogenies

of the photosystem II subunit III and the ribosomal protein L1; two genes of bona fide plastidic origin

(encoded in the plastid genome of Cyanophora paradoxa [24]). The branching pattern of eukaryotic

sequences in Fd-NIR and the two plastidic genes phylogenies suggest an early-branching

cyanobacterial lineage as the donor in all cases (Supplementary Figs 3, 4 and 5). Notwithstanding

160 whether plastids originated from an early or a deep cyanobacterial lineage [24,25], we interpret the

similar phylogenetic relationships between eukaryotes and Cyanobacteria in all our phylogenies as

moderate support for a plastidic origin for Fd-nir. In all the sampled taxa we found Fd-nir in genomic

sequences corresponding to the nuclear genome. This indicates that Fd-nir would have been

transferred to the nucleus before the divergence of all primary algal lineages, as indeed occurred

165 with many proteins of plastidic activity [10].

A cyanobacterial origin is unlikely for NAD(P)H-nir and nrt2 (Fig 3). In the NAD(P)H-NIR phylogeny

(Fig 3 and Supplementary Fig 6), the sister-group position of Planctomycetes to all eukaryotes

suggest that this cytoplasmic nitrite reductase originated in eukaryotes through a HGT from this

170 marine bacterial group. Finally, the phylogeny of NRT2 does not support any particular bacterial

lineage as the donor of this nitrate transporter to eukaryotes (Fig 3 and Supplementary Fig 7).

EUKNR originated by gene fusion

In contrast to Fd-nir, NAD(P)H-nir and nrt2, the distribution of euknr is restricted to eukaryotes. The

175 exclusive combination of protein domains shown by this nitrate reductase suggests a chimeric origin

involving the fusion of different proteins. Hence, we used a sequence similarity network-based

approach [2] to investigate which ancestral protein families were involved in EUKNR origins. A first

network between EUKNR and similar eukaryotic and prokaryotic sequences was constructed (Fig

4A; see Materials and methods section for details about the network construction process). The

180 topology of the network shows five different clusters, each one representing a specific protein family,

namely, bacterial sulfite oxidases (SUOX), eukaryotic SUOX with a Cytochrome b5 (Cyt-b5) domain,

eukaryotic SUOX without a Cyt-b5 domain, EUKNR, and NADH reductases (Fig 4A). The pattern

connecting the EUKNR with the eukaryotic SUOX and NADH reductase clusters is characteristic of

composite genes [26]; in which two unrelated gene families are connected in the network through

185 an intermediate gene family. This suggests that EUKNR shares homology with both eukaryotic

SUOX and NADH reductases [2]. Hence, a gene fusion between eukaryotic SUOX and NADH

reductases would account for the origin of respectively the N-terminal and C-terminal EUKNR

domains.

190 In the represented network, only eukaryotic SUOX without a Cyt-b5 domain are connected to

EUKNR. This suggests that EUKNR are more related to SUOX without a Cyt-b5, a result in

agreement with standard phylogenetic methods (EUKNR sequences branched closer to SUOX

without Cyt-b5; see Supplementary Fig 8). To determine the origin of the Cyt-b5 region, we used the

Cyt-b5 domain of the two EUKNR reference sequences to construct a second network including

195 those eukaryotic and prokaryotic proteins that aligned to this specific EUKNR region (Fig 4C). The

two Cyt-b5 EUKNR regions connected with a lower E-value with Cyt-b5 monodomain proteins than

with proteins whose architectures contain other domains in addition to Cyt-b5 (e.g. SUOX). This

strongly suggests that the Cyt-b5 region of EUKNR was not acquired from SUOX but rather

originated from a third protein. We thus propose that EUKNR has a chimeric origin, evolving from a

200 fusion of genes belonging to three distinct families: eukaryotic SUOX (without Cyt-b5), Cyt-b5

monodomain proteins, and NADH reductases.

Evaluating the impact of HGT in NAPs evolution

Some of the topologies shown in the phylogenies of NAPs (Fig 5) strongly disagree with the

205 eukaryotic species tree (Fig 2), and hence would require a large number of ancestral paralogues

and differential paralogue losses to be accounted by a strictly vertical inheritance scenario. In general

(and with the exception of nrt2, see below), there is usually one copy of NAP genes per genome

(see Supplementary Table 1). Therefore, we did not find any a priori reasons to hypothesize that the

number of copies could have been greater in the ancestral genomes. To evaluate potential cases of

210 HGT, we performed AU tests [27] (see all tested topologies and AU-test results in Supplementary

Table 3), as well as additional phylogenetic inferences excluding conflicting taxa and increasing the

taxon sampling by incorporating orthologues from the taxon-rich Marine Microbial Eukaryotic

Transcriptome Sequencing Project (MMETSP) dataset [28] (MMETSP trees, see Materials and

methods section).

215

Fd-NIR

This chloroplastic nitrite reductase is restricted to photosynthetic groups including all the primary

algal groups (Glaucophyta, Rhodophyta, Chloroplastida), which belong to the Archaeplastida

supergroup, as well as most of the sampled complex plastid algal groups, with the exception of the

220 two photosynthetic myzozoans sampled (Alveolata, SAR). These complex plastid algal groups

include Haptophyta, Ochrophyta (Stramenopiles, SAR), Bigellowiella natans (Chlorarachniophyta,

Rhizaria, SAR), and Guillardia theta (Cryptophyta, Archaeplastida) (Figs 2 and 5).

In the inferred phylogenetic tree, Galdieria sulphuraria (Rhodophyta) Fd-NIR is the earliest branch

225 within the eukaryotic clade (Fig 5, Supplementary Fig 9), in disagreement with the accepted

eukaryotic tree (Fig 2). However, the low nodal support and the fact that it branches with other

Rhodophyta sequences in the MMETSP tree suggest that this position is artefactual (Supplementary

Fig 10). Surprisingly, sequences from three Chloroplastida branch together with sequences from

Chondrus crispus and Pyropia yezoensis (Rhodophyta), and are hence separated from the rest of

230 Chloroplastida (we rejected the monophyly of Chlorophyta) (p-AU 0.0019). This unexpected topology

is also observed and well supported in the MMETSP tree, suggesting that it is unlikely to represent

a phylogenetic artefact. Because we showed that all eukaryotic Fd-nir descend from a unique

transfer from Cyanobacteria (Fig 4), this conflicting topology could only be explained either by

ancestral duplication and differential paralogue loss or by HGT.

235

All Fd-NIR sequences from Ochrophyta, Chlorarachniophyta and Haptophyta form a monophyletic

clade that branch within Archaeplastida, with strong support in the MMETSP tree (99% UFBoot). We

rejected a topology constraining the monophyly of all Archaeplastida sequences (p-AU 0.0009).

These results, together with Fd-NIR being a plastidic enzyme, supports a common origin of both Fd-

240 nir and plastids in these complex plastid algal groups. The phylogenetic position of Haptophyta

sequences within Ochrophyta is in agreement with recent studies suggesting an Ochrophyta origin

of the Haptophyta plastid [29,30] (we rejected the monophyly of Ochrophyta sequences) (p-AU

0.0029). The position of Chlorarachniophyta Fd-NIR within Ochrophyta, however, is more difficult to

explain. One could argue that this is due to low phylogenetic signal given that Chlorarachniophyta is

245 the closest group to Ochrophyta among the taxa with Fd-NIR. In fact, we could not reject an

alternative topology representing a vertical inheritance of Fd-nir in these two groups from a SAR

common ancestor (B. natans as sister-group to the Ochrophyta + Haptophyta clade) (p-AU 0.2318).

However, we consider the HGT scenario more parsimonious since the same topology was recovered

in both the MMETSP tree and NRT2 tree (Fig 5, see below).

250

NAD(P)H-NIR

This cytoplasmic nitrite reductase is distributed in two eukaryotic supergroups, Opisthokonta and

SAR (Figs 2 and 5). Within Opisthokonta, this gene is present in Fungi and Teretosporea; while in

SAR, we found it in Labyrinthulea and Oomycota (Stramenopiles) and in some of their photosynthetic

255 relatives from Ochrophyta (Stramenopiles) and Myzozoa (Alveolata). Again, the reconstructed

phylogeny shows a topology discordant with the eukaryotic species tree (Fig 2), with sequences

from Myzozoa, Ochrophyta and Labyrinthulea branching as the earliest clades, respectively, to a

clade including all Opisthokonta and Oomycota sequences (Fig 5). A hypothetical scenario that could

be proposed from this topology would imply that NAP(P)H-nir was transferred from Bacteria

260 (Planctomycetes, see Fig 3) to a common ancestor of Alveolata and Stramenopiles, then vertically

inherited in some Stramenopiles and transferred to Opisthokonta. Our test of alternative topologies

rejected the monophilies of Opisthokonta, Stramenopiles and Teretosporea (p-AU of 0.0022, 0.0002

and 0.0033, respectively). While this altogether supports HGTs involving these groups, the exact

number of transfers involving Opisthokonta and Stramenopiles lineages is uncertain. We thus

265 evaluate two parsimonious scenarios as potential explanations for the evolutionary history of

NAD(P)H-nir, which are based on three assumptions.

The first assumption is that NAD(P)H-nir originated in Opisthokonta from at least one HGT from

Stramenopiles. Although we could not reject a vertical inheritance of all Opisthokonta sequences

270 from a common eukaryotic ancestor (Stramenopiles + Opisthokonta clade as sister-group to other

eukaryotes) (p-AU 0.1387); we consider this as poorly parsimonious given the gene distribution and

the topology, not only of the NAD(P)H-NIR tree but also of other NAPs (Fig 5). The second

assumption is that a member of Labyrinthulea was involved in an HGT event to Opisthokonta, given

its sister-group position to the Opisthokonta + Oomycota clade (94% of UFBoot). Finally, a third

275 assumption is that there was an HGT event between Ichthyosporea and Oomycota, given that they

branch as sister-groups with high support (100% of UFBoot). Labyrinthulea and Oomycota are hence

the two Stramenopiles groups that we assume as potential donors of NAD(P)H-nir to Opisthokonta.

From this, we envision two parsimonious scenarios. A first one considers that all opisthokont

sequences descend from a single labyrinthulean transfer, which would imply that Ichthyosporea

280 subsequently transferred this gene to Oomycota. A second scenario considers that the transfer was

from Oomycota to Ichthyosporea, and hence that two different Stramenopiles lineages transferred

NAD(P)H-nir to Opisthokonta.

If the first scenario is correct, and Ichthyosporea transferred NAD(P)H-nir to Oomycota, a phylogeny

285 excluding Ichthyosporea should show the Oomycota sequences to be more related to other

Opisthokonta than to Ochrophyta (the closest taxonomic group to Oomycota in the NAD(P)H-NIR

dataset, see Fig 2). In agreement with this, a phylogeny excluding Ichthyosporea shows Oomycota

NAD(P)H-NIR branching within Opisthokonta with a strong support (UFBoot 96%, see

Supplementary Fig 11). Moreover, an Oomycota + Ochrophyta clade is rejected by the test of

290 alternative topologies (p-AU 0.0238). However, and unexpectedly, the same pattern did not occur

when we removed sequences from Oomycota, given that ichthyosporean sequences branch with

Labyrinthulea rather than with other Opisthokonta (Supplementary Fig 12). In this dataset without

Oomycota, we could not reject the topology forcing Ichthyosporea and Ochrophyta together (to be

expected if ichthyosporean sequences originated from the Stramenopiles lineage) (p-AU 0.0691).

295 However, given that the Ichthyosporea + Labyrinthulea clade is poorly supported (UFBoot 77%,

Supplementary Fig 12) and given that we rejected the Oomycota + Ochrophyta clade in the absence

of Ichthyosporea, we consider these results altogether more consistent with a transfer from

Ichthyosporea to Oomycota rather than in the opposite direction, thus supporting the first scenario

proposed (i.e. a transfer from Labyrinthulea to Opisthokonta, and then from Ichthyosporea to

300 Oomycota).

Lastly, we consider the unexpected position of Corallochytrium limacisporum (Corallochytrea,

Teretosporea) NAD(P)H-NIR within the fungal clade (Fig 5) as a phylogenetic artefact rather than as

a bona fide HGT event. First, the nodal support for the position is low (UFBoot 71%). In addition, C.

305 limacisporum appears as a long branch taxa [31] in phylogenomic analyses [32,33], and hence is a

problematic taxa when used in phylogenetic inferences. Moreover, topologies suggesting alternative

scenarios representing an independent origin of its NAD(P)H-nir from Fungi could not be excluded,

such as forcing the monophyly of fungal sequences or forcing the monophyly of C. limacisporum +

Ichthyosporea + Oomycota (p-AU 0.3787 and 0.1879, respectively).

310

NRT2

This nitrate transporter is widely distributed among eukaryotes with nitrate and nitrite reductase

genes (Supplementary Fig 2), with numerous species harboring lineage-specific duplications (see

blue dots in Supplementary Fig 13). In particular, we found 66 species-specific duplications among

315 the 56 species in which we found nrt2, with 36 duplication events occurring in Streptophyta

(Chloroplastida). Again, to reconcile the recovered topology with the eukaryotic tree (Fig 2), a strictly

vertical inheritance scenario would require a large number of ancestral duplications and differential

paralogue losses. While obvious nrt2 paralogues are observed (Supplementary Fig 13), these must

correspond to recent duplications given that sequences from the same species branch close to each

320 other. Therefore, as with other NAP genes, an HGT agnostic scenario would be poorly supported

given the absence of evident ancestral paralogues.

Sequences from Archaeplastida groups with primary plastids appear as the earliest clades of the

tree (Fig 5), together with other eukaryotes (we rejected the monophyly of all Archaeplastida

325 sequences) (p-AU 0.0008). The earliest-branching eukaryotic clade comprises only sequences from

Glaucophyta (UFBoot 100%). The other eukaryotic NRT2 sequences branch in two clades that are

strongly supported also in the taxon-rich MMETSP tree (Supplementary Fig 14). The first of these

two clades includes all the Chloroplastida and Haptophyta sequences. It is unclear whether

Haptophyta are more related to Chloroplastida [34] or to the SAR supergroup [35]. If Haptophyta

330 were more related to SAR, its position in this tree could be interpreted as a support for a horizontal

origin of nrt2 from Chloroplastida. Indeed, a previous study suggested that Haptophyta could have

received genes of non-plastidic function from the green-plastid lineage [36]. The second clade

includes Rhodophyta and Cryptophyta sequences branching as sister-group to a SAR +

Opisthokonta clade. Even though Cryptophyta presumably belongs to the Archaeplastida

335 supergroup, its position as sister-group to Rhodophyta is unexpected [34,35] and could represent

an ancestral Archaeplastida paralogue conserved in both groups. However, the plastid proteomes

of Cryptophyta show clear signatures of a Rhodophyta contribution [20,37], and hence nrt2 could

have been transferred to Cryptophyta from a red algal endosymbiont. Since a red algal signal has

also been found in some SAR plastid proteomes [20,37], we also propose a second transfer from

340 Rhodophyta to a SAR common ancestor; although we cannot discard an alternative scenario

involving a first transfer from Rhodophyta to Cryptophyta and then from Cryptophyta to a SAR

common ancestor (p-AU of 0.2698).

The topology within the SAR + Opisthokonta clade resembles that of the NAD(P)H-NIR tree (Fig 5).

345 Myzozoan sequences appear as the earliest-branching clade (Alveolata, SAR), with a clade

including Ochrophyta sequences (Stramenopiles, SAR) branching as sister-group to a clade

including the sequences from Oomycota and Labyrinthulea (Stramenopiles) and from Teretosporea

and Fungi (Opisthokonta). However, this tree also includes sequences from B. natans

(Chlorarachniophyta, Rhizaria, SAR) branching within the Ochrophyta clade, as in the Fd-NIR tree

350 (Fig 5). Given that additional Chlorarachniophyta sequences robustly branch as sister-groups to and

within Ochrophyta in the NRT2 and Fd-NIR MMETSP trees (Supplementary Figs 14 and 10,

respectively), we propose that these two NAP genes were co-transferred from Ochrophyta to

Chlorarachniophyta. Indeed, while all Chlorarachniophyta plastids presumably descend from a green

algal endosymbiont [20], the chimeric signal of their plastid proteome suggests that other algal

355 lineages could have contributed to the gene repertoire of this mixotrophic algal group [38].

As with the NAD(P)H-NIR phylogeny, our test of alternative topologies rejected the monophilies of

Opisthokonta, Stramenopiles and Teretosporea (p-AU 0.0246, 0.0028 and 0.0373, respectively).

This strongly supports HGT events involving these groups. There are two reasons in favor of at least

360 one HGT event from Stramenopiles to Opisthokonta. Firstly, as with NAD(P)H-NIR, the earliest

branching positions of other SAR lineages to the Stramenopiles + Opisthokonta clade suggests that

it is more likely that the first donor of the clade was a member of the Stramenopiles, which would

have inherited the genes from a common ancestor. Secondly, we rejected a topology compatible

with a vertical inheritance scenario of this gene in Opisthokonta from a common ancestor to all

365 eukaryotes (the Stramenopiles + Opisthokonta clade as sister-group to other eukaryotes, which

would imply an HGT origin of nrt2 in Labyrinthulea and Oomycota) (p-AU 0.0014).

In contrast to the NAD(P)H-NIR phylogeny, Labyrinthulea sequences do not branch as a sister-group

to Opisthokonta + Oomycota, appearing as the sister-group (together with C. limacisporum) to Fungi

370 (Fig 5). Based on this topology, one possible interpretation is that nrt2 could have originated in

Opisthokonta from an ancestral member of the Stramenopiles. Then, Oomycota and Labyrinthulea

would have acquired nrt2 from Ichthyosporea and from an ancestor of C. limacisporum, respectively;

instead of vertically inheriting nrt2 from that Stramenopiles ancestor. Because this hypothesis (H1)

is too outlandish and the accuracy of protein trees is limited [39], we evaluated the following

375 alternative potential scenarios for the origin of the nrt2 in Opisthokonta (Supplementary Fig 15): (H2)

nrt2 would have been transferred from (i) Oomycota to a common ancestor of Opisthokonta, and

then from (ii) an ancestor of C. limacisporum to Labyrinthulea; (H3) nrt2 would have been transferred

from (i) Labyrinthulea to a common ancestor of Opisthokonta, and then from (ii) Ichthyosporea to

Oomycota -the more parsimonious history for NAD(P)H-nir-; (H4) same as H3, but (ii) with Oomycota

380 as a donor of the transfer to Ichthyosporea; and (H5) two labyrinthulean transfers would have

occurred: a first transfer to common ancestor of Fungi and a second transfer to an ancestor of C.

limacisporum. In this scenario, Oomycota would have transferred nrt2 to Ichthyosporea.

We discarded the hypothesis H2 given its incompatibility with the molecular clock-based divergence

385 times proposed for the evolution of eukaryotes [40]. In particular, Oomycota could not have

transferred nrt2 to a common ancestor of Teretosporea and Fungi because these two lineages would

have diverged before Oomycota originated [40]. However, we could not discard any of the other

hypotheses (detailed below). As with NAD(P)H-NIR, if H3 was true (the p-AU for this topology is

0.1818), we would expect the sequences from Oomycota to be more related to a Opisthokonta +

390 Labyrinthulea clade rather than to Ochrophyta in a tree without Ichthyosporea (Supplementary Fig

16). The same applies for the ichthyosporean sequences in a tree without Oomycota (Supplementary

Fig 17). If, however H4 or H5 were true, we would expect exactly the opposite topology (i.e.

Oomycota more related to Ochrophyta in the absence of Ichthyosporea, and vice versa).

Unfortunately, the topologies recovered show contradictory results (Supplementary Fig 16 and 17).

395 To conclude, even though H3 could be favored given that it is the most parsimonious hypothesis for

NAD(P)H-NIR phylogeny (see previous Results section), neither H4 nor H5 can be rejected, at least

by the phylogenetic signal of NRT2.

EUKNR

400 The distribution of euknr was found to be very similar to that of nrt2 (Supplementary Fig 2). Euknr is

present in most photosynthetic and non-photosynthetic organisms for which we inferred the

capability to assimilate nitrate (Figs 2 and 5). Interestingly, we found the euknr (but no other NAP

genes) also in Chromosphaera perkinsii (Ichthyosporea, Opisthokonta). The presence of euknr in

an additional ichthyosporean besides Creolimax fragrantissima and Sphaeroforma arctica may be

405 an indicator that their NAP genes were vertically inherited from an opisthokont ancestor and

subsequently lost in the other ichthyosporeans, many of which have been described as parasitic

species [41]. This was the scenario proposed by the hypothesis H3 (Supplementary Fig 15).

Unfortunately, the phylogenetic signal does not allow to confidently infer the evolutionary history of

this gene, including the eukaryotic lineage in which this nitrate reductase would have had originated

410 (Fig 5 and Supplementary Fig 18).

Notwithstanding the weak support of the phylogeny, we found three unexpected and well- supported

relationships between distantly related taxa. Firstly, Oomycota branches as the sister-group to the

ichthyosporeans C. fragrantissima and S. arctica, as in the NRT2 and NAD(P)H-NIR trees (UFBoot

415 95%). This strongly indicates that a transfer of the whole pathway occurred between Oomycota and

Ichthyosporea. Secondly, there is a clade that comprises several distantly related fungal sequences

as well as a sequence from Acanthamoeba castellanii (Amoebozoa). However, sequences from

these fungal taxa are also found in another clade that includes the A. nidulans sequence of bona

fide nitrate reductase activity (named Anid_NaR in the euk_db dataset) [42][43]. Moreover, there is

420 experimental evidence excluding that the A. nidulans euknr paralogue could function as a nitrate

reductase [44] (Kaufmann, J. Fritz, D. Canovas, M. Gorfer and J. Strauss, personal communication).

Thus, we propose that a fungal paralogue of euknr, of uncertain function, was transferred from an

ancestral fungus to a lineage leading to A. castellanii. In fact, the finding of a gene transfer in A.

castellanii is not surprising considering the extensive signatures of HGT found in this early

425 amoebozoan lineage. Thirdly, B. natans branches in-between Chlorophyta, in agreement with its

plastid being originated from a green algal endosymbiont [20].

Origin and evolution of NAP clusters

We then inquired the importance of NAP clustering in shaping the evolution of this pathway. To this

430 end, we analyzed the distribution of the clusters within the eukaryotic tree (Fig 2). We found clusters

in >56% of the sampled eukaryotes with at least two NAP genes in the genome (Supplementary

Table 1). In particular, clusters were patchily distributed in Fungi, Teretosporea, Oomycota,

Ochrophyta, Labyrinthulea, Myzozoa, Chlorarachniophyta, Chlorophyta, Rhodophyta and

Haptophyta. The patchy distribution of the clusters within these groups suggests that many de-

435 clustering events had occurred, assuming that de-clustering events are more parsimonious than de

novo clustering events. NAP genes are always found unclustered in Cryptophyta, Glaucophyta and

Streptophyta. While Cryptophyta and Glaucophyta are poorly represented in our dataset, the

absence of clusters in Streptophyta (includes land plants) is remarkable since NAPs are found in the

9 sampled genomes of this group (Supplementary Table 1).

440

We found that >64% of the detected clusters include the whole pathway, nrt2, euknr and either

NAD(P)H-nir or Fd-nir. In Ochrophyta, the only eukaryotic group with taxa showing both nitrite

reductases in the same genome, we found clusters comprising nrt2 or euknr and either Fd-nir or

NAD(P)H-nir, but never both (Fig 2). In agreement with the gene distribution, clusters with Fd-nir are

445 found only in autotrophs. While clusters with NAD(P)H-nir are also found in autotrophs, in particular

in two Ochrophyta (Stramenopiles, SAR) and in one Myzozoa (Alveolata, SAR) species; they are

mostly distributed along osmotrophic taxa from Oomycota and Labyrinthulea (Stramenopiles, SAR)

and from Fungi and Teretosporea (Opisthokonta) (NAP clusters with NAD(P)H-nir hereafter

abbreviated as hNAPc, for “heterotrophic NAP clusters”).

450

The presence in two of the three primary algal groups of NAP clusters including Fd-nir leads to two

potential scenarios. First, we can envision a unique origin of the cluster in an archaeplastidan

ancestor. If Glaucophyta, where the NAPs are not clustered (Fig 2), was an earlier lineage than

Rhodophyta and Chloroplastida [24], cluster formation could have occurred in the last common

455 ancestor of Rhodophyta and Chloroplastida. If so, at least two de-clusterization events would have

occurred: one in the lineage leading to C. crispus and P. yezoensis (Rhodophyta) and the other in

the lineage leading to Streptophyta (Chloroplastida) (Fig 2). A second scenario would imply at least

two independent clustering events, in the lineages leading to Cyanidioschyzon merolae and G.

sulphuraria (Rhodophyta) and to Chlorophyta (Chloroplastida).

460

The tendency of NAP genes to be clustered in green and red algae lineages may have facilitated

the transfer of the entire pathway during the endosymbiotic events involving these algal groups [20].

However, the phylogenetic signal of NAPs suggests that not all the clusters in complex plastid algae

would have been acquired from a single endosymbiont, with at least two independent clustering

465 events occurring in the lineages leading to Chrysochromulina sp. (Haptophyta) and B. natans

(Chlorarachniophyta). In Chrysochromulina sp., the cluster would have had originated after the

acquisition of nrt2 and Fd-nir from Chloroplastida and Ochrophyta, respectively (Fig 5). In B. natans,

the cluster would have had originated after the acquisition of euknr and Fd-nir from Chloroplastida

and Ochrophyta, respectively.

470

For hNAPc, we propose that this cluster could had been transferred between heterotrophs given that

sequences from taxa bearing the cluster (Fig 2) branch close to each other in the NAP trees (Fig 5).

This would have allowed transfers of the entire metabolic pathway, which we consider more

parsimonious than individual transfers of the genes followed by multiple clusterization events. Thus,

475 in agreement with NRT2 and NAD(P)H-NIR phylogenies, we propose that hNAPc would had been

originated in a common ancestor of Alveolata and Stramenopiles and later transferred between

Stramenopiles and Opisthokonta. The phylogenetic signal does not allow to infer the number and

direction of hNAPc transfers that had occurred between Stramenopiles and Opisthokonta.

480 A tetrapyrrole methylase and the origin of NAPs in Opisthokonta

Given the uncertainty of the phylogenetic signal, we searched for additional features that could help

clarify which of the proposed hypotheses for the origin of hNAPc in Opisthokonta is more

parsimonious (Supplementary Fig 15). We checked intron positions, but we found them to be poorly

conserved and not useful to clarify phylogenetic relationships (data not shown). We found, however,

485 in the genomes of C. limacisporum, C. fragrantissima (Teretosporea, Opisthokonta) and

Aplanochytrium kerguelense (Labyrinthulea, Stramenopiles, SAR) an additional protein annotated

with a TP_methylase Pfam domain clustering with NAP genes. The three proteins showed highest

similarity to Uroporphyrinogen-III C-methyltransferases (data not shown), a class of tetrapyrrole

methylases involved in the biosynthesis of siroheme (which works as a prosthetic group for many

490 enzymes, NAD(P)H-NIR included) [45]. A phylogenetic tree of this protein family showed a clade

that includes the three proteins clustered with NAP genes as well as other eukaryotic proteins

branching within a bacterial clade (Supplementary Figs 19 and 20). We, therefore, consider this

group a subfamily of eukaryotic tetrapyrrole methylases, hereafter referred as “TPmet”.

495 We showed that NAP phylogenies support an origin of NAP genes in Opisthokonta through a transfer

of hNAPc from Stramenopiles. Under this hypothesis, the finding of tpmet clustered with NAP genes

(tpmet-hNAPc) in three Opisthokonta and Labyrinthulea taxa could suggest that tpmet may have

been co-transferred in cluster with NAP genes also from Stramenopiles to Opisthokonta. If so, we

could expect the phylogeny and the distribution of tpmet to resemble that of hNAPc and the

500 corresponding genes. While the inferred tree is poorly informative given the low nodal support values

(Supplementary Fig 20), the distribution of tpmet shows similarities with the distribution of hNAPc. In

particular, we found tpmet in ~93% of taxa encoding NAD(P)H-nir, the defining gene of the cluster

(see the previous Results section). However, only ~55% of the taxa with tpmet have NAD(P)H-nir.

Interestingly, almost all the ~45% of taxa with tpmet that do not have NAD(P)H-nir correspond to

505 Opisthokonta lineages without NAP genes, such as Nucleariidae, Choanoflagellata as well as many

ichthyosporeans (Supplementary Fig 21). Thus, if tpmet emerged in Opisthokonta through a tpmet-

hNAPc transfer, its presence in these early lineages would reinforce the single transfer scenario to

a common ancestor of Opisthokonta from Stramenopiles, being NAP genes secondarily lost in those

taxa. Moreover, the presence of tpmet-hNAPc in C. limacisporum (Corallochytrea, Teretosporea)

510 and C. fragrantissima (Ichthyosporea, Teretosporea) favors a vertical inheritance of tpmet-hNAPc in

Corallochytrea and Ichthyosporea from a common teretosporean ancestor rather than a horizontal

origin of the ichthyosporean NAP genes from Oomycota; given that tpmet is not clustered with NAP

genes in any Oomycota genome. Overall, among all the proposed scenarios, we propose H3 as the

most parsimonious given the phylogenetic signal of NAPs and the distributions of tpmet and tpmet-

515 hNAPc (see all the scenarios evaluated in Supplementary Fig 15).

A novel chimeric nitrate reductase in ichthyosporean NAP clusters

In C. fragrantissima and S. arctica, rather than the canonical nitrate reductase, we identified a gene

clustered with nrt2 and NAD(P)H-nir that has a chimeric domain architecture consisting of (i) the first

520 three Pfam domains of the EUKNR in the N-terminal region; and (ii) the first two Pfam domains of

the NAD(P)H-NIR in the C-terminal region (Fig 6A). A domain architecture analysis of proteins from

euk_db and prok_db (see Materials and methods section) showed this unexpected domain

architecture to be restricted to these two ichthyosporeans. Phylogenetic analyses showed that the

region containing the Oxidoreductase molybdopterin binding, Mo-co oxidoreductase dimerisation

525 and Cytochrome b5-like Heme/Steroid binding Pfam domains correspond to the EUKNR family (Fig

5 and Supplementary Fig 18), and includes the nitrate reducing module characteristic of this nitrate

reductase [46]. In contrast, the C-terminal region, corresponding to the Pfam domains Pyridine

nucleotide-disulphide oxidoreductase and BFD-like [2Fe-2S] binding domain, branched within the

NAD(P)H-NIR clade in a tree including all the eukaryotic and prokaryotic proteins containing this pair

530 of domains (Fig 6B and Supplementary Fig 22). In that tree, the two sequences branched as sister-

group to C. fragrantissima and S. arctica NAD(P)H-NIR proteins. Therefore, we propose that this

chimeric gene originated after the replacement of the canonical C-terminal EUKNR region by the N-

terminal region of the NAD(P)H-NIR in a common ancestor of these two ichthyosporeans (hereafter

we refer to this gene as C. fragrantissima and S. arctica putative nitrate reductase, abbreviated as

535 CS-pNR). This event should have occurred after the HGT event involving Ichthyosporea and

Oomycota, since the nitrate reductase found in Oomycota does comprise the canonical domain

architecture of EUKNR (Fig 6A).

S. arctica has a NAP cluster functional for nitrate assimilation

540 We sought for experimental evidence of nitrate assimilation in S. arctica, as a representative of an

ichthyosporean NAP cluster including the putative uncharacterized nitrate reductase (CS-pNR). We

developed a minimal growth medium in which the nitrogen source (N source) can be controlled

(‘modified L1 medium – mL1’, see Materials and methods). We then tested growth of S. arctica in

mL1 minimal medium with different N sources (Fig 7A). In all the minimal medium conditions (mL1

545 + different N sources), cells were smaller than in Marine Broth, used as the positive control. We

observed a slight growth in the negative control (‘mL1’) after 168 hours, which we hypothesize can

be due to the use of cell reserves, or the utilization of vitamins from the medium as N source. We

detected a clearly stronger growth in mL1 supplemented with either NaNO3, (NH4)2SO4 or urea,

compared to mL1 without any N source. The growth observed in mL1 + NaNO3 shows that S. arctica

550 is able to assimilate nitrate.

The finding that S. arctica can grow using nitrate as the sole N source implies that this organism

must have a nitrate reductase activity, and the CS-pNR is indeed a strong candidate to carry out this

enzymatic activity, in line with the bioinformatics evidence (Fig 6). In general, NAP genes from

555 different eukaryotic species had been shown to be co-regulated in response to environmental N

sources [19,47–50]. Hence, a co-regulated expression of CS-pnr with nrt2 and NAD(P)H-nir would

be consistent with their proposed role in nitrate assimilation. We thus measured the levels of

expression of the three genes in S. arctica, in the presence of different N sources (Fig 7B). The three

S. arctica genes were up-regulated either in mL1 without any N source as well as in mL1 + NaNO3.

560 In contrast, we observed that the three genes were poorly expressed in mL1 + (NH4)2SO4 and in

mL1 + urea. These results show that the cluster is functional in S. arctica and also that its expression

is regulated in response to different N sources.

Discussion

Nitrate assimilation is restricted to autotrophs and fungal-like osmotrophs

565 Our screening of NAP genes provides an updated and comprehensive picture of the distribution of

the nitrate assimilation pathway in eukaryotes (Fig 2). Besides the taxa included in previous studies

[14,51], we describe the presence of the complete pathway in Haptophyta, Cryptophyta,

Chlorarachniophyta, Myzozoa, Labyrinthulea and Teretosporea (Supplementary Fig 1). While all

autotrophs analyzed have NAP genes, this is not the case for heterotrophs, where we only found

570 NAP genes in taxa from those groups that have convergently evolved into a fungus-like osmotrophic

lifestyle [21], that is Fungi, Ichthyosporea, Oomycota and Labyrinthulea (Fig 2 and Supplementary

Fig 2). The absence of this pathway in phagotrophs is probably due to the fact that this nutrient

acquisition strategy provides access to organic nitrogen sources, whose incorporation is

energetically less demanding than nitrate. Thus, NAP genes would be less likely to be acquired and

575 more prone to be lost in phagotrophic lineages, as presumably occurred with genes involved in the

synthesis of certain amino acids [52].

HGT and the evolutionary history of NAPs in eukaryotes

The patchy distribution of this metabolic pathway (Fig 2) and the large number of non-vertical

580 relations observed in our phylogenies (Fig 5) are not consistent with an exclusive scenario of vertical

transmission and gene loss. We consider that some of the unexpected topologies found represent

indeed bona fide gene transfers, because we consistently recovered them in more than one NAP

phylogeny and/or because they fit with endosymbiotic events proposed for the acquisition of complex

plastids [10,37]. Here we detail our proposed evolutionary scenario to account for the distribution

585 and the phylogenetic signal of NAPs (Fig 8):

(1) Three of the four NAP genes originated in eukaryotes through independent transfers from

Bacteria. The nitrite reductases NAD(P)H-nir and Fd-nir were most likely transferred from

Planctomycetes and Cyanobacteria (Fig 3), respectively; with Fd-nir showing signatures of a plastidic

590 origin (Supplementary Fig 3) if, as proposed, this organelle originated from an early-cyanobacterial

lineage [25,53]. The particular bacterial donor of the nitrate transporter nrt2 remains unclear (Fig 3).

The nitrate reductase euknr originated through the fusion of three eukaryotic genes: a sulfite oxidase,

a Cyt-b5 monodomain and a FAD/NAD reductase (Fig 4). Furthermore, we hypothesize that the

pathway, including nrt2, Fd-nir and euknr, was established in an early-Archaeplastida ancestor, as

595 discussed below. First, the three pathway activities most likely originated in the same eukaryotic

ancestor. If this is the case, and the plastidic nitrite reductase Fd-NIR, and not NAD(P)H-NIR, was

present in the original nitrate assimilation toolkit, this would imply an Archaeplastida origin of the

pathway, given that it is well established that plastids originated in this group. The phylogenies of

Fd-NIR and NRT2 are consistent with this hypothesis, as they show Archaeplastida sequences in

600 the earliest branches within eukaryotes (Fig 5). The fact that the same topology is not observed in

the EUKNR tree does not contradict our argument, since the EUKNR tree showed low statistical

nodal support (Supplementary Fig 18). The alternative NAD(P)H-nir-early scenario, while still

possible, is less parsimonious because it disagrees with the NRT2 phylogeny and requires of

additional secondary losses of this gene.

605

(2) We propose that NAP genes were transferred from Archaeplastida to other eukaryotic groups

during the endosymbiotic events that led to the origin of complex plastids, as it has been shown for

numerous genes not necessarily related to plastidic functions [10]. Consistent with this, our

phylogenies suggest multiple NAP transfers between algal lineages (Fig 8), with sequences from the

610 complex plastid algal groups branching as sister-groups to the early-branching Archaeplastida

sequences in the Fd-NIR and NRT2 trees (Fig 5). For some transfers, the donor and the receptor

lineages coincide with proposed endosymbiotic events. This is the case of euknr from Chlorophyta

to Chlorarachniophyta [20], Fd-nir from Ochrophyta to Haptophyta [30] and nrt2 from Rhodophyta to

Cryptophyta and to SAR [20]. Even though we also found some unexpected transfers between algal

615 lineages, we also consider them as potential endosymbiotic gene transfers. The reason is that the

origin of complex plastids is not clearly elucidated, partly due to the heterogeneous phylogenetic

signal shown by the plastid proteomes [37]. Based on this heterogeneity, the target-ratchet model

proposes that complex plastids resulted from a long-term serial association with different transient

endosymbionts, all of which could have contributed in shaping the proteome of the host lineage [20].

620 Consistent with this model, we found NAP genes in Haptophyta and Chlorarachniophyta that would

have been transferred from different potential algal endosymbionts (Fig 8).

(3) From the gene distribution and the phylogenies (Fig 5), we parsimoniously propose that

NAD(P)H-nir was transferred from Planctomycetes to a common ancestor of Alveolata and

625 Stramenopiles. The advent of this cytoplasmic nitrite reductase would have resulted in a eukaryotic

nitrate assimilation pathway independent from Fd-NIR, and hence independent of the chloroplast.

We found NAP sequences from distinct osmotrophic lineages from Stramenopiles and Opisthokonta

branching together in the trees (Fig 5), strongly suggesting HGT events involving these groups.

Based in these phylogenies (Fig 5) but also in an analysis of the distribution and the gene

630 composition of the clusters (Figs 2 and 6), we parsimoniously propose a first transfer of a NAP cluster

from an ancestral stramenopiles (probably from Labyrinthulea) to a common opisthokont ancestor;

and a second transfer of a cluster from Ichthyosporea (Teretosporea) to Oomycota (Stramenopiles)

(see H3 and all the scenarios evaluated in Supplementary Fig 15). NAP genes would had been

subsequently lost in multiple opisthokonts, mostly in phagotrophs but also in some ichthyosporean

635 and fungal groups (Fig 8). Interestingly, the role of HGT in shaping the gene toolkits for osmotrophic

functions is well documented in Oomycota and Fungi [12,54]. Our finding of HGT events involving

taxa from these two groups but also from Teretosporea and Labyrinthulea extends the scope and

potential importance of this mechanism in the acquisition of metabolic features associated to an

osmotrophic lifestyle [21].

640

The hypothetical scenario that we propose for the origin of nitrate assimilation in Opisthokonta

disagrees with previous results from Slot and Hibbet [14]. They recovered Oomycota as sister-group

to Fungi, while in our trees with an updated taxon-richer dataset, Oomycota branches as sister-group

to Ichthyosporea within the Opisthokonta + Stramenopiles clade (Fig 5). To evaluate whether the

645 discrepancies with previous studies are the result of differences in the taxon sampling, we

constructed trees excluding all Teretosporea and Labyrinthulea sequences. In agreement with the

results of Slot and Hibbet, we then recovered the Oomycota sequences branching as sister-group

to Fungi in the NRT2 and NAD(P)H-NIR phylogenies (Supplementary Figs 23 and 24, respectively).

To be compatible with the molecular clock data [40] and the phylogenetic signal (Fig 5), an Oomycota

650 origin of all NAP genes in Opisthokonta would require multiple transfers from this lineage, and hence

it is poorly parsimonious (see H6 in Supplementary Fig 15). Instead, in agreement with the H3

scenario, we propose that in the results of Slot and Hibbet, Oomycota (Stramenopiles) appeared

more related to Fungi (Opisthokonta) than to Ochrophyta (Stramenopiles) because Oomycota

received the NAP genes from Opisthokonta, in particular from Ichthyosporea. Notwithstanding, the

655 support for the proposed scenario is susceptible to change with the addition of further taxa, given

the dependence of HGT inference to the taxon sampling used [7].

HGT of NAPs could be favored by the metabolic, genomic and ecological

landscapes

660 While HGT in eukaryotes has been the subject of controversy, there is an increasing number of gene

families where HGT has been shown to play a role [11,55,56]. The results presented here show the

evolutionary history of the nitrate assimilation pathway as a striking example of the importance that

gene transfer between eukaryotes may have in the evolution of a certain metabolic pathway. Among

the transfers proposed by the most parsimonious scenario (Fig 8), we consider at least the following

665 ones as bona fide transfers because of being well supported by the data (see Results section): 1) At

least one transfer of a NAP cluster from an ancestral stramenopiles to Opisthokonta; 2) a NAP cluster

transfer from Ichthyosporea to Oomycota or vice versa (although the first is more parsimonious); 3)

a nrt2 transfer between Haptophyta and Chlorophyta; 4 and 5) a Fd-nir transfer from primary algae

to SAR, and from Ochrophyta to Haptophyta; 6) a euknr transfer from Chlorophyta to

670 Chlorarachniophyta; and 7) a transfer of a euknr paralogue of unknown function from Fungi to a

lineage leading to A. castellanii.

We argue that NAP genes may be particularly prone to be successfully transferred. On a metabolic

level, pathways downstream to nitrate assimilation and the enzymes involved in the synthesis of the

675 molybdenum cofactor (required for the activity of a number of enzymes, EUKNR included) are

widespread in eukaryotes [46,52,57]. This would facilitate the functional coupling of the newly

transferred pathway to the metabolic network. On a genomic level, NAP genes are frequently

organized in gene clusters in eukaryotic genomes (Fig 2). This would allow the acquisition of the

whole pathway in a single HGT event [58], which is also more likely to be positively selected than

680 separate transfers of individual components of the pathway. Moreover, the presence of the whole

pathway in the same genomic region could also favor the evolution of a co-regulated transcriptional

control after the HGT acquisition [59]. There are various reported examples of other metabolic gene

clusters transferred between eukaryotes [60]. On an ecological level, nitrate concentrations have

been fluctuating in the course of evolutionary history [61], and are still highly dependent on regional

685 and seasonal changes [16]. Thus, in some circumstances NAP genes could be dispensable while in

other circumstances their acquisition through HGT would be favored. This dynamic evolutionary

fitness could imply that even one given eukaryotic lineage could have acquired and lost the faculty

of nitrate assimilation more than once in the course of its evolution.

690 Nitrate assimilation in Ichthyosporea: a putative novel nitrate reductase

The presence of NAP genes in Ichthyosporea, described as animal symbionts or parasites [41] and

phylogenetically related to Metazoa [32], was not previously reported. In the NAP clusters of C.

fragrantissima and S. arctica, we found a putative nitrate reductase gene that probably originated in

the common ancestor of these two ichthyosporeans (CS-pnr) from the fusion of the N-terminal region

695 of the EUKNR with the C-terminal region of the NAD(P)H-NIR (Fig 6). The presence of the nitrate

reducing module characteristic of EUKNR [46] strongly suggests the clustered CS-pNR is a

functional nitrate reductase. The growth on nitrate as sole nitrogen source of S. arctica (mL1 +

NaNO3, Fig 7A), in the absence of any other candidate enzyme in the genome, constitutes almost

definitive proof for this function. This is further supported for by the strong transcriptional co-

700 regulation of CS-pnr with nrt2 and NAD(P)H-nir in response to the availability of different nitrogen

sources. In particular, these genes are poorly expressed on easily assimilable nitrogen sources (urea

and ammonium) and highly expressed in nitrogen-free medium as well as in the presence of nitrate

(Fig 7B).

705 The results from the RT-qPCR experiments can be most easily rationalized by a straight-forward

repression process. However, specific induction by nitrate cannot be excluded. In the nicotinate

assimilation pathway of A. nidulans, we see both specific induction and high expression under

nitrogen starvation conditions, mediated by the same transcription factor [62]. It is possible that in

this latter instance the intracellular inducer is generated by degradation of intracellular metabolites.

710 Similarly, in the absence of any added nitrogen source, a high affinity nitrate transporter may

scavenge residual nitrate present in the nitrate-free culture medium, as it has been specifically shown

for A. nidulans [63], Hansenula polymorpha [64] and C. reinhardii [65]. In agreement with this,

RNAseq data show that in A. nidulans, an organism where the nitrate-responsive transcription factor

has been thoroughly studied [63], nitrate starvation results in high expression of the three genes in

715 the NAP cluster [66].

The transcriptional regulation of NAPs has been characterized in land plants [47], Chlorophyta [19],

Rhodophyta [48], Fungi [49,50]; and now also in the ichthyosporean S. arctica (Fig 7). The

independent origins of NAP genes in some of these groups (Fig 8), together with the shown lineage-

720 specific differences at the regulatory elements [19,67–69] suggests that natural selection promoted

the evolution of analogous regulatory responses, favoring the integration of this pathway into the

metabolic landscape after its acquisition through HGT.

725 Materials and methods

Phylogenetic screening of NAPs

An updated database of 174 eukaryotic proteomes (euk_db) was constructed (January 2017), using

predicted protein sequences from publicly available genomic or transcriptomic projects [70–72]. The

complete list of species, with the corresponding abbreviations, is available in Supplementary Table

730 1. All supplementary tables are in Supplementary File 2; supplementary files are accessible in

https://figshare.com/s/d11b23d7928009e2d508). The phylogenetic relationships between all the

sampled eukaryotes were constructed from recent bibliographical references (James et al., 2006;

Ruhfel et al., 2014; Derelle et al., 2015; Sierra et al., 2015; Kurtzman et al., 2015; Derelle et al.,

2016; He et al., 2016; Janouškovec et al., 2017; Kang et al., 2017; Mccarthy and Fitzpatrick, 2017;

735 Muñoz-Gómez et al., 2017; Brown et al., 2018). Protein domain architectures from all euk_db

sequences were obtained with PfamScan (a Hidden Markov Model [HMM] search-based tool) using

Pfam A version 29 [85]. A database of prokaryotic protein sequences (prok_db) was constructed

from Uniprot bacterial and archaeal reference proteomes (Release 2016_02) [72] with the aim of

detecting potential prokaryotic contamination in euk_db as well as to investigate the prokaryotic

740 origins of eukaryotic NAP genes.

For each NAP, we followed a multi-step procedure in order to maximize both sensitivity and

specificity in the orthology assignation process (see Supplementary File 1 for detailed information

about the particular strategy followed for each NAP). The overall strategy consisted first in identifying

745 potential NAP family members in euk_db with BLAST (version 2.3.0+) [86] and HMMER (version

3.1b1) [87]. For BLASTP searches, we queried the databases using the NAP sequences from

Chlamydomonas reinhardtii and A. nidulans [18], downloaded from Phytozome 11 [88] and NCBI

protein databases [70], respectively [BLASTP: -evalue 1e-5, only non-default software parameters

specified]. For HMMER searches [hmmsearch], we used the HMM Pfam domains MFS_1 for NRT2,

750 Oxidored_molyb and Mo-co_dimer for EUKNR, and NIR_SIR for NAD(P)H-NIR and Fd-NIR. The

candidate sequences retrieved from the BLASTP and hmmsearch analyses were submitted to cdhit

(version 4.6) [89] [-c 0.99] to remove repeated/very recent paralogues (i.e. redundant sequences).

We used the non-redundant candidate sequences to detect potential prokaryotic homologues in

prok_db [-evalue 1e-5], to use them as outgroups to eukaryotic sequences and/or to detect potential

755 euk_db contaminant sequences during the phylogenetic analyses. The non-redundant candidate

sequences and the captured prokaryotic homologs were submitted to an iterative process in which

we recursively performed phylogenetic inferences with the sequences non-discarded in the previous

steps until we reached a set of bona fide NAP family members. The criteria to discard sequences in

each step was mainly phylogenetic, but also assisted with functional information of each candidate

760 sequence, predicted from their Pfam domain architecture and from their best-scoring BLASTP hit [-

evalue 1e-3] against the SwissProt database [72] (downloaded on July 2016). Those potential

eukaryotic NAPs that branched separately from other eukaryotic sequences within a prokaryotic

clade in the phylogenies were considered as contaminants if they correspond to a euk_db proteome

generated from transcriptomic data obtained from cultures with bacterial contamination, or if they are

765 encoded in potentially contaminant genomic scaffolds. Previous to all phylogenetic inferences,

sequences were aligned with MAFFT (version v7.123b) [90] [mafft-einsi] and alignments were

trimmed with trimAl (version v1.4.rev15) [91] using the -gappyout option. Maximum likelihood

phylogenetic inference was done using RAxML (version 8.2.4) [92] with rapid bootstrap analysis (100

replicates) and using the best model according to BIC criteria in ProtTest analyses (version 3.2) [93].

770

In Supplementary Table 1, for each species, the columns corresponding to NAPs are colored in blue

when at least 1 bona fide member has been identified. They are colored in light brown when all

members identified are likely to correspond to bacterial contamination, and in red when no NAPs

were identified.

775

Re-annotation of NAPs using TBLASTN

For those eukaryotes in which we detected an incomplete presence of the pathway (i.e. having only

genes coding for some but not the three required steps, see Fig 1), we performed additional searches

in the genomic sequences of the corresponding organism using the reference NAP protein

780 sequences [TBLASTN: -evalue 1e-5]. This additional search allowed us to re-annotate two putative

NAPs absent from euk_db (Fd-NIR in Aureococcus anophagefferens and NRT2 in Ostreococcus

tauri) that were later incorporated in the phylogenies.

We also searched for potentially transferred prokaryotic nitrate and nitrite reductases, whose

785 presence would suggest a replacement of their eukaryotic counterparts. While a putative ‘Copper

containing nitrite reductase’ was found in the amoebozoan Acanthamoeba castellanii, we considered

this sequence as an uncharacterized copper oxidase not necessarily involved in nitrite reduction.

We were based in the fact that (1) the most similar sequences in euk_db and prok_db correspond

to few distantly related eukaryotes without any NAPs or with already the complete eukaryotic

790 pathway predicted such as C. reinhardtii and (2) the absence of the characteristic InterPro Nitrite

reductase, copper-type signature.

Correlation between NAPs distribution and feeding strategies

We constructed phylogenetic profiles for each NAP gene family: vectors with presence/absence

795 information (coded in “1” or “0”, respectively), with every position of the vectors corresponding to a

certain species sampled in our euk_db dataset. These vectors were then used to quantify the

correlation between the distributions of the different NAPs by computing the inverse of the Hamming

distance between each pair of phylogenetic profiles. We also quantified the correlation between the

distribution of the different NAPs and the distribution of the different nutrient acquisition strategies in

800 eukaryotes. For that, we classified eukaryotes into ‘Autotrophs/Mixotrophs’ (i.e. strictly and

facultative autotrophs) and ‘Non-autotrophs’. ‘Non-autotrophs’ (i.e. strictly heterotrophs) were further

subclassified into ‘Phagotrophs’, ‘Fungal-like osmotrophs’ and ‘Others’ (Supplementary Table 1).

The category ‘Phagotrophs’ include all heterotrophs that feed by phagotrophy. The category ‘Fungal-

like osmotrophs’ include all heterotrophs that belong to eukaryotic groups with cellular and

805 physiological features characteristic of a fungal-like osmotrophic lifestyle [21]. These include Fungi,

Teretosporea, Oomycota and Labyrinthulea. The category ‘Others’ include all the heterotrophs not

classified in any of these categories, all of them belonging to eukaryotic groups with a parasitic

lifestyle.

810 Evolution of NAP genes

We used the bona fide eukaryotic NAP sequences identified to reconstruct the evolutionary history

of the NAP gene families in eukaryotes. We excluded all the sequences with less than half of the

median length of the corresponding NAP family in order to remove fragmented sequences that could

mislead the alignment and the phylogenetic inference processes. Sequences were aligned and

815 trimmed with MAFFT [mafft-einsi] and trimAl [-gappyout]. For the phylogenies, we used IQ-TREE

(version 1.5.3) [94] instead of RAxML given that an approximately unbiased (AU) test can be

performed in IQ-TREE [27]. AU test was used to evaluate whether the robustness of those branches

indicating potential gene transfer events are significantly higher than other alternative topologies

(10000 replicates; see all the alternative topologies tested and AU test results in Supplementary

820 Table 3). Trees representing the alternatives topologies were constructed also with IQ-TREE, using

the same alignments and evolutionary models and constraining the topologies with Newick guide

tree files [-g option]. For bootstrap support assessment, we used the ultrafast bootstrap option (1000

replicates) because was shown to be faster and less biased than standard methods [95,96]. For

model selection, we used ModelFinder, already implemented in IQ-TREE [97].

825

Moreover, and given that some eukaryotic groups were poorly represented due to the lack of

genomic data, we constructed additional NAP trees incorporating orthologues from the Marine

Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) dataset [28]. We queried the

reference NAP protein sequences against all the MMETSP transcriptomes [BLASTP: -evalue 1e-3].

830 MMETSP NAP orthologues were identified from the aligned sequences by means of Reciprocal Best

Hits (RBH) [98] and best-scoring BLASTP hit against SwissProt database [-evalue 1e-3].

Comprehensive screening of NAPs in prokaryotes

We used the bona fide eukaryotic NAP sequences to capture potential prokaryotic orthologues of

835 nrt2, NAD(P)H-nir and Fd-nir. First, we queried those sequences against prok_db with BLASTP [-

max_target_seqs 100, -evalue 1e-5]. Protein domain architectures were annotated with PfamScan,

and those with clearly divergent architectures were discarded. The remaining prokaryotic sequences

were aligned with eukaryotic NAPs using MAFFT [mafft-einsi]. The alignments were trimmed with

trimAl [-gappyout] and the phylogenetic inferences were done with IQ-TREE [ultrafast bootstrap 1000

840 replicates, best model selected with ModelFinder]. Prokaryotic sequences were taxonomically

characterized by aligning them against a local NCBI nr protein database (downloaded on November

2016), and only hits with more than 99% of identity and query coverage were considered [BLASTP:

-task blastp-fast].

845 To ensure that the taxonomic representation of prok_db allow to detect signatures of genes likely to

have been transferred from Alphaproteobacteria and Cyanobacteria (the putative donors of the

mitochondria and the plastid, respectively [99]), we constructed control phylogenies using in each

case two genes with a known plastidic (‘Photosystem II subunit III’ and ‘ribosomal protein L1’ [24])

(Supplementary Figs 4 and 5, respectively) and mitochondrial origin (‘Cytochrome c oxidase subunit

850 III’ and ‘Cytochrome b’ [100]) (Supplementary Figs 25 and 26, respectively). For the mitochondrial

and plastid control genes, the eukaryotic sequences used to query prok_db were retrieved from a

subset of proteomes from plastid-bearing eukaryotes. For the detection of potential orthologues in

prok_db, alignment and phylogenetic inference; we used the same procedure, software and

parameters than with the NAP trees (see above).

855

Construction of sequence similarity networks

Sequence similarity network of full length EUKNR

The EUKNR protein sequences were aligned against a database including euk_db and prok_db

[BLASTP: -max_target_seqs 10000, -evalue 1e-3]. Aligned sequences were concatenated with the

860 EUKNR and redundant sequences were removed with cdhit before being aligned all-against-all with

BLASTP [-max_target_seqs 10000, -evalue 1e-3]. We used Cytoscape (version v.321) [89] to

construct a sequence similarity network from BLAST results, represented using the organic layout

option. In the network, each aligned protein correspond to a node. Nodes are connected through

edges if the corresponding sequences aligned with a lower E-value than the threshold value. A

865 relaxed E-value threshold would lead to an over-connected network, with edges connecting very

divergent proteins. On the other hand, a strong threshold would lead to an under-connected network,

having only connections between strongly similar proteins. After exploring different thresholds, we

chose an E-value of 1e-82 because it allows to represent only the most similar protein families to the

N-terminal and C-terminal regions of EUKNR. We performed as well the following modifications in

870 order to remove redundant and non-informative connections and to facilitate the analysis and

interpretation of the network: (i) we removed self-loops and duplicate edges; (ii) we removed those

nodes that were not connected to the EUKNR cluster or that were connected with a distance of more

than two nodes; (iii) non-EUKNR sequence names were modified to include information of their

protein domain architectures [PfamScan]; (iv) we removed nodes and edges corresponding to

875 proteins with strong evidence of corresponding to miss-predicted proteins (e.g. spurious domain

architectures). Nodes representing proteins that only connected with miss-predicted sequences

were also removed (information about the list of proteins, their domain architecture and the particular

reasons for their exclusion is available in Supplementary Table 2).

880 To validate whether EUKNR are more phylogenetically related to non-Cyt-b5 sulfite oxidases than

to Cyt-b5 sulfite oxidases (see the corresponding Results section), we constructed a phylogenetic

tree with the identified EUKNR sequences and the sulfite oxidases detected during the network

construction process. MAFFT [mafft-einsi], trimAl [-gappyout] and IQ-TREE [ultrafast bootstrap 1000

replicates, best model selected with ModelFinder] were used for phylogenetic inference.

885

Sequence similarity network of EUKNR Cyt-b5 domain

The regions of the A. nidulans and C. reinhardtii EUKNR corresponding to the Cyt-b5 Pfam domain

were aligned against a database including euk_db and prok_db [BLASTP: -max_target_seqs 10000,

-evalue 1e-3]. Non-redundant and non-EUKNR sequences were concatenated with the two EUKNR

890 Cyt-b5 sequences and an all-against-all alignment was performed [BLASTP: -max_target_seqs

10000, -evalue 1e-3]. Sequence names were modified to include information of their protein Pfam

domain architectures [PfamScan]. A sequence similarity network was constructed with Cytoscape

and represented with the organic layout option (as with full length EUKNR), removing self-loops and

duplicate edges and using an E-value threshold of 1e-17. We also removed those nodes that were

895 not connected to A. nidulans or C. reinhardtii EUKNR Cyt-b5 regions or that were connected with a

distance of more than two nodes.

Detection of NAP clusters

For the detection of clusters of NAP genes, we scanned the genomes of those sampled eukaryotes

900 with more than 1 NAP gene identified. We aligned the NAPs of each organism against the

corresponding genomes using TBLASTN [-evalue 1e-3]. The genomic location of each NAP was

annotated based on the TBLASTN hit with the highest score. Then, we looked for genomic fragments

with more than 1 NAP genes annotated, and the genes were considered to be in a cluster when they

were proximally located in that fragment. In the case of Corallochytrium limacisporum, the two NAP

905 genes detected were found in terminal positions of two separate fragments of the genome assembly

(nrt2 in scaffold99_len85036_cov0 and NAD(P)H-nir in scaffold79_len158446_cov0). To figure out

whether these two genes are in different scaffolds because of an assembly artifact, we designed

primers directed to the terminal regions of both fragments (ClimH_R73C and ClimH_F72C, see all

the primers used in this work in Supplementary Table 4). These primers were used to check, by

910 PCR, whether the two scaffolds are contiguous on the same chromosome. We obtained a PCR

fragment of ~500 bp that was cloned into pCR2.1 vector (Invitrogen) and Sanger sequenced. BLAST

analysis of the sequenced products (available in Supplementary Table 4) showed the presence of

regions from both scaffolds in the extremes of the PCR fragment, confirming that nrt2 and NAD(P)H-

nir are clustered in this species.

915

Furthermore, we investigated the genomic regions flanking the clusters of C. fragrantissima, S.

arctica, C. limacisporum, Phytophthora infestans and A. kerguelense in order to find additional genes

in the NAP clusters of Opisthokonta and SAR. Because we found a TP_methylase Pfam domain

protein (TP_methylase) clustered with NAP genes in three of these genomes, we scanned the

920 remaining SAR and Opisthokonta for the presence of additional clusters of NAP genes with a

TP_methylase. To do that, we retrieved all the TP_methylase of each organism and aligned them

against the corresponding genome [TBLASTN: -evalue 1e-3]. As with NAP genes, the genomic

location of each TP_methylase was annotated considering the BLAST hit with the highest score.

925 Phylogenetic analyses of tetrapyrrole methylase proteins

All the TP_methylase in euk_db were retrieved and used to detect similar sequences in prok_db

[BLASTP: 1e-3]. Among the aligned sequences from prok_db, only those with a detected

TP_methylase Pfam domain were kept [PfamScan]. TP_methylase sequences from euk_db and

prok_db were aligned with MAFFT and trimmed with trimAl [-gappyout]. Because there were >1000

930 sequences in the alignment, we used FastTreeMP (version 2.1.9) [101] for the construction of the

phylogenetic tree instead of IQ-TREE. We kept for further analyses the sequences in the blue clade

because it included the three TP_methylase proteins found in cluster with NAP genes (sequences

pointed by arrows in Supplementary Fig 19). Because in that blue clade eukaryotic sequences were

monophyletic and branched within a bacterial clade, we considered all the eukaryotic sequences of

935 this clade as a particular eukaryotic TP_methylase protein family (TPmet). We used all TPmet

sequences to capture potential prokaryotic homologs of this specific family in prok_db [BLASTP: -

evalue 1e-3], which were incorporated to TPmet sequences for a second phylogenetic tree

(Supplementary Fig 27). To that end, sequences were aligned with MAFFT [mafft-einsi], trimmed

with trimAl [-gappyout], and the tree was inferred with IQ-TREE [ultrafast bootstrap 1000 replicates,

940 best model selected with ModelFinder]. To get a higher phylogenetic resolution of TPmet and their

prokaryotic relatives, a third and last phylogenetic inference (Supplementary Fig 20) was done with

sequences labeled in blue in Supplementary Fig 27 (for phylogenetic inference, we used the same

procedure as for the second tree).

945 We also constructed a Venn diagram to evaluate the coincidence between the phylogenetic

distributions of TPmet and NAD(P)H-nir families along eukaryotes. In this analysis, we excluded the

TPmet sequence belonging to N. vectensis (Nvec_XP_001617771) because it is located in a

genomic fragment (NW_001825282.1) that most likely represents a contaminant scaffold. In

particular, the phylogenetic tree revealed that this protein is identical to a region of the TPmet found

950 in the choanoflagellate Monosiga brevicollis (Mbre_XP_001745780). We found that this M.

brevicollis protein, as well as the TPmet protein found for the choanoflagellate Salpingoeca rosetta

(Sros_PTSG_11107), are encoded in large genomic fragments (1259938 bp in the case of M.

brevicollis), while the N. vectensis protein is found in a small genomic fragment (1325 bp). Moreover,

this N. vectensis fragment entirely aligned without mismatches with the M. brevicollis fragment

955 (CH991551, between the 280127-281451 positions), indicating that this most likely represents a

contamination from the M. brevicollis genome.

Phylogenetic analyses of the C-terminal region of CS-pNR

Sequences from euk_db and prok_db as well as from MMETSP and Microbial Dark Matter database

960 (MDM_db) [102] (downloaded in January 2017) were scanned for the co-presence Pyr_redox_2 and

Fer2_BFD Pfam domains [hmmsearch]. Sequences with these pair of domains were retrieved and

aligned with MAFFT [mafft-einsi]. We only kept the region of the alignment that correspond to

Pyr_redox_2 and Fer2_BFD Pfam domains. The alignment was further trimmed with trimAl [-

gappyout], and IQ-TREE was used for the phylogenetic inference [ultrafast bootstrap 1000

965 replicates, best model selected with ModelFinder].

Cells and growth conditions

S. arctica JP610 was grown axenically at 12 ºC in 25 cm2 or 75 cm2 culture flasks (Corning) filled,

respectively, with 5 mL or 20 mL of Marine Broth (Difco). For nitrogen limitation experiments, cells

970 were incubated in modified L1 medium (mL1) [103], of the following composition (per liter): 35 g

-5 marine salts (Instant Ocean), 0.1 g dextrose, 5 g NaH2PO4.H2O, 1.17 x 10 M Na2EDTA.2H2O, 1.17

-5 -7 -8 -8 x 10 M FeCl3.6H20, 9.09 x 10 M MnCl2.4H20, 8.00 x 10 M ZnSO4.7H20, 5.00 x 10 M CoCl2.6H20,

-8 -8 -8 -8 1 x 10 M CuSO4.5H20, 8.22 x 10 M Na2MoO4.2H2O, 1 x 10 M H2SeO3, 1 x 10 M NiSO4.6H20, 1

-8 -8 -8 -10 -11 x 10 M Na3VO4, 1 x 10 M K2CrO4, 2.96 x 10 M thiamine·HCl, 2.05 x 10 M biotin, 3.69 x 10 M

975 cyanocobalamin. For nitrogen supplementation experiments, mL1 medium was supplemented with

either 100 mM NaNO3, 100 mM (NH4)2SO4 or 100 mM urea as nitrogen source, as specified in the

text. Photomicrographies were taken with a Nikon Eclipse TS100 equipped with a DS-L3 camera

control unit (Nikon). Images were processed with imageJ.

980 RNA isolation, cDNA synthesis and real-time PCR analyses

The expression levels of S. arctica NAP genes in cultures with different nitrogen sources were

analyzed using real-time PCR. S. arctica cells were grown for 10 days in 75 cm2 cell culture flasks

(Corning) with 20 mL Marine Broth (Difco). Cells were scraped and collected by centrifugation at

4500 xg for 5 min at 12 ºC in 50 mL Falcon tubes (Corning). Supernatant was discarded and pellets

985 were washed twice by resuspension with 20 mL of mL1 medium to wash out any trace of Marine

Broth. An aliquot of the washed cells was collected as time 0. Cells were finally resuspended in mL1

medium, distributed equally into four 25 cm2 culture flasks, and supplemented with different nitrogen

sources. Aliquots were collected at 6, 12 and 24 hours. At each time-point, cells were pelleted in 15

mL Falcon tubes (Corning), supernatant was discarded and the pellets were resuspended in 1 mL

990 Trizol reagent (Invitrogen) and transferred to 1.5 mL microfuge tubes with safe lock (Eppendorf).

Tubes were subjected to two cycles of freezing in liquid nitrogen and thawing at 50 ºC for 5 min.

After this treatment, samples were kept at -20 ºC until further processing. To eliminate any trace of

genomic DNA, total RNA was treated with Amplification Grade DNAse I (Roche) and precipitated

with ethanol in the presence of LiCl. The absence of genomic DNA was confirmed using a control

995 without reverse transcription. A total of 2.5 µg of pure RNA was used for cDNA synthesis using oligo

dT primer and SuperScript III retrotranscriptase (Invitrogen), following the instructions of the

manufacturer. cDNA was quantified using SYBR Green supermix (Bio-Rad) in an iQ cycler and iQ5

Multi-color detection system (Bio-Rad). Primer sequences are shown in Supplementary Table 4. The

total reaction volume was 20 µL. All reactions were run in duplicate. The program used for

1000 amplification was: (i) 95 ºC for 3 min; (ii) 95 ºC for 10 s; (iii) 60 ºC for 30 s; and (iv) repeat steps (ii)

and (iii) for 40 cycles. Real-time data was collected through the iQ5 optical system software v. 2.1

(Bio-Rad). Gene expression levels are expressed as number of copies relative to the ribosomal L13

subunit gene, used as housekeeping.

1005 Acknowledgements

We thank José Luis Maestro for his help in qPCR design and qPCR results interpretation, Meritxell

Antó for technical assistance, and Michelle Leger for their valuable comments on the manuscript.

EOP also warmly acknowledge the MCG C. Committee for their insightful advice and final approval

of figures design. This work was supported by an ERC Consolidator Grant (ERC-2012-Co-616960),

1010 support from the Secretary's Office for Universities and Research of the Generalitat de Catalunya

(project 2014 SGR 619) and one grant from the Spanish Ministry for Economy and Competitiveness

(MINECO; BFU2014-57779-P, with European Regional Development Fund support), all to IRT. SRN

is a member of the Carrera del Investigador Científico from CONICET, Argentina. EOP was

supported by a pre-doctoral FPI grant from MINECO.

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Fig 1. Proteins involved in the eukaryotic nitrate assimilation pathway (NAPs). The eukaryotic

nitrate assimilation pathway and the downstream proteins necessary for the assimilation of

1275 ammonium. Nitrate transporter NRT2; EUKNR: assimilatory NAD(P)H:nitrate reductase [EC 1.7.1.1-

3]; NAD[P]H-NIR: ferredoxin-independent assimilatory nitrite reductase [EC 1.7.1.4]; Fd-NIR:

ferredoxin-dependent assimilatory nitrite reductase [EC 1.7.7.1]; GS: glutamine synthetase [EC

6.3.1.2], GOGAT: Glutamine oxoglutarate aminotransferase [1.4.1.14], GDH: Glutamate

dehydrogenase [EC. 1.4.1.2-4]. In this article, we focus on the proteins specifically required for the

1280 incorporation and reduction of nitrate to ammonium (hereafter abbreviated as NAPs, for “Nitrate

Assimilation Proteins”).

Fig 2. Distribution of NAP gene families among 172 sampled eukaryotic genomes. The

evolutionary relationships between the sampled species, represented in a cladogram, were

1285 constructed from recent bibliographical references (see Materials and methods section). Species

names were colored according to the taxonomic groups to which they belong. The presence of each

NAP in each taxon is shown with symbols. Black symbols indicate genes that are found within

genome clusters of NAP genes. For illustration purposes, some clades of species (e.g. Metazoa)

were collapsed into a single terminal leaf. For detailed information about the taxonomic categories

1290 and the NAP profiles and NAP cluster status of each species, see Supplementary Table 1.

Autotrophic and fungal-like osmotrophic lineages are indicated (see panel and see Supplementary

Table 1 for information about the nutrient acquisition strategy of each taxon).

Fig 3. The prokaryotic origins of nrt2, NAD(P)H-nir and Fd-nir shown by phylogenetic

1295 analyses. Schematic representation of the maximum likelihood phylogenetic trees inferred for nrt2,

NAD(P)H-nir and Fd-nir, with the aim of reconstructing the origins of the eukaryotic homologs.

Prokaryotic sequences were taxonomically characterized following NCBI taxonomic categories.

Clades with bacterial sequences belonging to the same taxonomic group were collapsed and colored

as indicated in the panel. Similarly, eukaryotic sequences were classified, collapsed and colored

1300 according to whether they contain or not a plastid/plastid-related organelle. See Supplementary Figs

3, 6 and 7 for the entire representation of phylogenetic trees and Materials and methods section for

details on their reconstruction.

Fig 4. The chimeric origin of euknr shown by sequence-similarity network approach. Graphical

1305 representation of two pre-processed sequence similarity networks constructed from all-vs-all Blast

hits between eukaryotic and prokaryotic proteins. Sequences were detected using as queries all

eukaryotic EUKNR in (A) and the Cytochrome-b5 (Cyt-b5) regions of Chlamydomonas reinhardtii

and Aspergillus nidulans (reference EUKNR sequences) in (C). See Materials and methods section

for details on the network pre-processing and construction processes. Each node represents a

1310 protein, and each edge represents a Blast hit between two proteins. Proteins were grouped and

colored according to their protein domain architecture and protein family information (see panels). In

(C), we also represented the lowest E-value with which C. reinhardtii aligned with the Cyt-b5

monodomain and the Cyt-b5 multidomain clusters (see Results section). (B) The canonical protein

domain architecture of a full-length eukaryotic EUKNR (Pfam domains), with paired lines indicating

1315 the gene families from which each domain would have originated (see Results section). Bact:

Bacterial. SUOX: sulfite oxidase. Euk: Eukaryotic. Prot: Protein. EUKNR: eukaryotic nitrate

reductase. NADH red: NADH reductase. Cyt-b5: Cytochrome b5-like Heme/Steroid binding Pfam

domain. Crei: Chlamydomonas reinhardtii. Anid: Aspergillus nidulans. Oxidored_molyb:

Oxidoreductase molybdopterin binding Pfam domain. Mo-co_dimer: Mo-co oxidoreductase

1320 dimerization Pfam domain. FAD_binding_6: Ferric reductase NAD binding Pfam domain.

NAD_binding_1: Oxidoreductase NAD-binding Pfam domain.

Fig 5. The evolutionary history of NAPs in eukaryotes. Simplified representation of the maximum

likelihood phylogenetic trees inferred for each NAP (Fd-NIR, NAD[P]H-NIR, NRT2, EUKNR). Some

1325 branches were collapsed into clades that represent higher eukaryotic taxonomic groups. Branches

and clades were colored according to the taxonomic groups to which they belong (see panel). For

illustration purposes, given the overall poor nodal support of the EUKNR tree, we converted the

branches with <90% UFBoot into polytomies using Newick Utilities (Junier et al., 2010) (see the draft

EUKNR tree in Supplementary Fig 18).

1330

Fig 6. NAP clusters in Ichthyosporea and the origins of a putative novel nitrate reductase. (A)

Cluster organization and protein domain architecture of NAP clusters from some holozoan and

stramenopiles representatives. Within each cluster each box represents a gene, with the arrowhead

indicating its orientation. The Pfam domains predicted for the corresponding protein sequences are

1335 represented inside each box (see panel). (B) Schemes showing a simplified representation of the

maximum likelihood phylogenetic trees inferred for the N-terminal and C-terminal regions of the

putative nitrate reductase identified in Creolimax fragrantissima and Sphaeroforma arctica (CS-pNR,

see Results section). For an entire representation of the phylogenetic trees, see Supplementary Figs

18 and 22 for N-terminal and C-terminal regions, respectively. (C) Schematic representation of the

1340 evolutionary origin of CS-pnr, inferred from the phylogenies shown in (B).

Fig 7. Sphaeroforma arctica culture and qPCR experiments in nitrogen minimal media. (A)

Growth of Sphaeroforma arctica in media with different nitrogen sources (scale bar = 100 µm). (B)

S. arctica NAP genes mRNA levels in mL1, mL1 + NaNO3, mL1 + (NH4)2SO4 and mL1 + urea. The

1345 y-axis represents copies per copy of ribosomal L13. Results are expressed as the mean ± S.D. of

three independent experiments.

Fig 8. Summary of the HGT events that we propose to have occurred in the evolution of NAP

genes in eukaryotes. Each NAP gene is represented by a specific symbol (same as Fig 2; see

1350 panel). Donor and receptor lineages as well as the NAP genes involved in each transfer are

indicated. Transfers of NAP genes in clusters are represented with the corresponding NAP symbols

surrounded by a square. Branches in red are those where loss of the entire pathway would have

occurred, which were parsimoniously inferred from the reconstructed evolutionary history. Lineages

are colored according to the taxonomic group to which they belong (see panel). For the sake of

1355 simplicity, some species were collapsed into clades representing higher taxonomic categories. For

each species/clade, NAP gene presence/absence (NAP symbols) and their cluster status (symbols

colored in black for those NAPs found in a same gene cluster) are indicated. For those clades in

which not all the represented species have the same NAP content and cluster status (labeled with

*), the most prevalent ones are shown (see Supplementary Table 1 for a complete representation of

1360 the NAP content and cluster status).

Supplementary files captions

All supplementary files are accessible in https://figshare.com/s/d11b23d7928009e2d508. These

include:

1365 Supplementary File 1. Supplementary methods for the 'Phylogenetic screening of NAPs' section.

Supplementary File 2. Includes all the supplementary tables.

Supplementary figures captions

Supplementary Fig 1. Completeness of the nitrate assimilation pathway in the 172 sampled

1370 eukaryotic genomes. The evolutionary relationships between the sampled species, represented in a

cladogram, were constructed from recent bibliographical references (see Materials and methods

section). Species names were colored according to the taxonomic groups to which they belong. The

presence of each NAP in each taxon is shown with symbols. Black symbols indicate genes that are

found within genome clusters of NAP genes. For illustration purposes, some clades of species (e.g.

1375 Metazoa) were collapsed into a single terminal leaf. For detailed information about the taxonomic

categories and the NAP profiles and NAP cluster status of each species, see Supplementary Table

1. Species are labelled as to whether they include a complete (dark blue circle) or partial pathway

(light blue circle). The presence of the pathway was considered complete when the transporter and

the two reductase activities (i.e. NRT2, EUKNR and at least 1 of the two NIRs) were detected in the

1380 genome.

Supplementary Fig 2. Correlation measures of NAPs distribution. (A) Correlation (from 0 to 1)

between the distributions of the four NAPs in the entire eukaryotic dataset and (B) in eukaryotes

from which at least one NAP was identified. (C) Correlation between the presence of NAPs with the

1385 nutrient acquisition strategies within the entire eukaryotic dataset (from 0 to 1) (see Materials and

methods section).

Supplementary Fig 3. Maximum likelihood phylogenetic tree inferred from eukaryotic and

prokaryotic Fd-NIR amino acid sequences. The tree was rooted in the branch that separates the

1390 eukaryotic clade from the rest of the tree. Statistical support values (1000-replicates UFBoot) are

shown in all nodes. Prokaryotic sequences were colored according to the corresponding phylum or

class, while eukaryotes were colored according to whether they contain or not a plastid/plastid-

related organelle (see panel).

1395 Supplementary Fig 4. Maximum likelihood phylogenetic tree inferred from eukaryotic and

prokaryotic 'Photosystem II subunit III' amino acid sequences (plastidic protein). Statistical support

values (1000-replicates UFBoot) are shown for all nodes. Prokaryotic sequences were colored

according to the corresponding phylum or class, while eukaryotes were colored according to whether

they contain or not a plastid/plastid-related organelle (see panel).

1400

Supplementary Fig 5. Maximum likelihood phylogenetic tree inferred from eukaryotic and

prokaryotic 'Ribosomal protein L1' amino acid sequences (plastidic protein). Statistical support

values (1000-replicates UFBoot) are shown for all nodes. Non-informative clades were collapsed.

Prokaryotic sequences were colored according to the corresponding phylum or class, while

1405 eukaryotes were colored according to whether they contain or not a plastid/plastid-related organelle

(see panel).

Supplementary Fig 6. Maximum likelihood phylogenetic tree inferred from eukaryotic and

prokaryotic NAD(P)H-NIR amino acid sequences. The tree was rooted in the branch that separates

1410 the eukaryotic clade from the rest of the tree. Statistical support values (1000-replicates UFBoot) are

shown in all nodes. Prokaryotic sequences were colored according to the corresponding phylum or

class, while eukaryotes were colored according to whether they contain or not a plastid/plastid-

related organelle (see panel).

1415 Supplementary Fig 7. Maximum likelihood phylogenetic tree inferred from eukaryotic and

prokaryotic NRT2 amino acid sequences. The tree was rooted in the branch that separates the

eukaryotic clade from the rest of the tree. Statistical support values (1000-replicates UFBoot) are

shown for all nodes. Prokaryotic sequences were colored according to the corresponding phylum or

class, while eukaryotes were colored according to whether they contain or not a plastid/plastid-

1420 related organelle (see panel).

Supplementary Fig 8. Schematic representation of a maximum likelihood phylogenetic tree

including the identified EUKNR and SUOX sequences. The sulfite oxidases (SUOX) sequences were

detected during the EUKNR sequence-similarity network reconstruction process. The topology

1425 suggests that EUKNR sequences are more related to SUOX without a Cyt-b5 domain, in agreement

with the network results.

Supplementary Fig 9. Maximum likelihood phylogenetic tree inferred from eukaryotic Fd-NIR amino

acid sequences, with some prokaryotic sequences used as outgroup (see Materials and methods

1430 section). The tree was rooted in the branch that separates the eukaryotic clade from the bacterial.

Statistical support values (1000-replicates UFBoot) are shown in all nodes. Eukaryotic sequence

names are abbreviated with the four-letter code (see Supplementary Table 1) and colored according

to their major taxonomic group (see panel). All sequences starting with 'UP-' correspond to

prokaryotic sequences.

1435

Supplementary Fig 10. Maximum likelihood phylogenetic tree inferred from eukaryotic Fd-NIR

amino acid sequences, with some prokaryotic sequences used as outgroup and including sequences

from the MMETSP dataset (see Materials and methods section). The tree was rooted in the branch

that separates the eukaryotic clade from the prokaryotic sequences. Statistical support values (1000-

1440 replicates UFBoot) are shown for all nodes. Eukaryotic sequence names from euk_db are

abbreviated with the four-letter code (see Supplementary Table 1) and colored according to their

major taxonomic group (see panel). Sequences from MMETSP are colored in black. All sequences

starting with 'UP-' correspond to prokaryotic sequences.

1445 Supplementary Fig 11. Maximum likelihood phylogenetic tree inferred from eukaryotic NAD(P)H-

NIR, with some prokaryotic sequences used as outgroup and excluding Creolimax fragrantissima

and Sphaeroforma arctica sequences. The tree was rooted in the branch that separates the

eukaryotic clade from the bacterial sequences, with nodes. Statistical support values (1000-

replicates UFBoot) are shown for all nodes. Eukaryotic sequence names are abbreviated with the

1450 four-letter code (see Supplementary Table 1) and colored according to their major taxonomic group

(see panel). All sequences starting with 'UP-' correspond to prokaryotic sequences.

Supplementary Fig 12. Maximum likelihood phylogenetic tree inferred from eukaryotic NAD(P)H-

NIR, with some prokaryotic sequences used as outgroup and excluding the sequence from

1455 Phytophthora infestans. The tree was rooted in the branch that separates the eukaryotic clade from

the bacterial sequences, with nodes. Statistical support values (1000-replicates UFBoot) are shown

for all nodes. Eukaryotic sequence names are abbreviated with the four-letter code (see

Supplementary Table 1) and colored according to their major taxonomic group (see panel). All

sequences starting with 'UP-' correspond to prokaryotic sequences.

1460

Supplementary Fig 13. Maximum likelihood phylogenetic tree inferred from eukaryotic NRT2, with

some prokaryotic sequences used as outgroup. The tree was rooted in the branch that separates

the eukaryotic clade from the bacterial sequences. Statistical support values (1000-replicates

UFBoot) are shown in all nodes. Eukaryotic sequence names are abbreviated with the four-letter

1465 code (see Supplementary Table 1) and colored according to their major taxonomic group (see panel).

All sequences starting with 'UP-' correspond to prokaryotic sequences. Nodes with blue circles

correspond to species-specific duplication events.

Supplementary Fig 14. Maximum likelihood phylogenetic tree inferred from eukaryotic NRT2 amino

1470 acid sequences, with some prokaryotic sequences used as outgroup and including sequences from

the MMETSP dataset (see Materials and methods section). The tree was rooted at the branch that

separates the eukaryotic clade from the bacterial sequences. Statistical support values (1000-

replicates UFBoot) are shown for all nodes. Eukaryotic sequence names from euk_db are

abbreviated with the four-letter code (see Supplementary Table 1) and colored according to their

1475 major taxonomic group (see panel). Sequences from MMETSP are colored in black. All sequences

starting with 'UP-' correspond to prokaryotic sequences.

Supplementary Fig 15. Six hypothetical scenarios evaluated for the origin and evolution of nrt2 and

other genes that were likely co-transferred in cluster between lineages of Stramenopiles and

1480 Opisthokonta. For each scenario, we indicate the branches in which gene transfer, clustering, de-

clustering and gene loss events are proposed to have occurred in the evolution of Alveolata and

Stramenopiles (left panel) and Opisthokonta (right panel). The proposed donors of the transfers are

also indicated. With the exception of Sphaeroforma arctica, Creolimax fragrantissima and

Corallochytrium limacisporum, the other species were grouped and the clades were named

1485 according to (i) the more inclusive taxonomical category of the taxa represented or (ii) with the four-

letter code of the taxa represented (see Supplementary Table 1). For each clade, a symbol of any of

the four inspected genes is represented if we detected them in at least one taxa of that clade.

Similarly, the largest cluster of TPmet + NAP genes found in each clade is indicated.

1490 Supplementary Fig 16. Maximum likelihood phylogenetic tree inferred from eukaryotic NRT2, with

some prokaryotic sequences used as outgroup and excluding Creolimax fragrantissima and

Sphaeroforma arctica sequences. The tree was rooted at the branch that separates the eukaryotic

clade from the bacterial sequences. Statistical support values (1000-replicates UFBoot) are shown

for all nodes. Eukaryotic sequence names are abbreviated with the four-letter code (see

1495 Supplementary Table 1) and colored according to their major taxonomic group (see panel). All

sequences starting with 'UP-' correspond to prokaryotic sequences.

Supplementary Fig 17. Maximum likelihood phylogenetic tree inferred from eukaryotic NRT2, with

some prokaryotic sequences used as outgroup and excluding sequences from Oomycota. The tree

1500 was rooted at the branch that separates the eukaryotic clade from the bacterial sequences. Statistical

support values (1000-replicates UFBoot) are shown in all nodes. Eukaryotic sequence names are

abbreviated with the four-letter code (see Supplementary Table 1) and colored according to their

major taxonomic group (see panel). All sequences starting with 'UP-' correspond to prokaryotic

sequences.

1505

Supplementary Fig 18. Maximum likelihood phylogenetic tree inferred from eukaryotic EUKNR, with

some sulfite oxidase sequences used as outgroup. The tree was rooted in the branch that separates

the EUKNR clade from the three sulfite oxidase sequences. Statistical support values (1000-

replicates UFBoot) are shown in all nodes. Eukaryotic sequence names are abbreviated with the

1510 four-letter code (see Supplementary Table 1) and colored according to their major taxonomic group

(see panel). All sequences starting with 'UP-' correspond to prokaryotic sequences.

Supplementary Fig 19. Maximum likelihood phylogenetic tree of TP_methylase Pfam domain

proteins from euk_db and prok_db (see Materials and methods section). Eukaryotic sequence

1515 names are abbreviated with the four-letter code (see Supplementary Table 1) and colored according

to their major taxonomic group (see panel). All sequences starting with 'UP-' correspond to

prokaryotic sequences. A second phylogenetic tree (Supplementary Fig 27) was constructed using

sequences from the blue clade (named as TPmet proteins, see Materials and methods section). The

three sequences found in cluster with NAP genes are indicated with arrows.

1520

Supplementary Fig 20. Phylogenetic inference of the tetrapyrrole methylase TPmet family.

Maximum likelihood phylogenetic tree of TP_methylase Pfam domain proteins (see Materials and

methods section), including all the sequences from the blue clades in Supplementary Fig 27. All the

eukaryotic sequences of the tree are considered to belong to a subset of tetrapyrrole methylase

1525 proteins named TPmet family. Eukaryotic sequence names are abbreviated with the four-letter code

(see Supplementary Table 1) and colored according to their major taxonomic group (see panel). All

sequences starting with 'UP-' correspond to prokaryotic sequences. The three sequences found in

cluster with NAP genes are indicated with arrows.

1530 Supplementary Fig 21. Distribution of TPmet in eukaryotes. Venn diagram representing the

quantitative distribution of the sampled eukaryotes (euk_db) recording the presence/absence of the

NAD(P)H-nir and the TPmet genes. A ranking of the taxonomic groups that have at least one

representative species with the TPmet but without the NAD(P)H-nir is also represented.

1535 Supplementary Fig 22. Maximum likelihood phylogenetic tree of the regions of all the euk_db,

prok_db, MMETSP and MDM_db proteins with the Pyr_redox_2 and Fer2_BFD Pfam domains (see

Materials and methods section). Eukaryotic sequence names are abbreviated with the four-letter

code (see Supplementary Table 1) and colored according to their major taxonomic group (see panel).

All sequences starting with 'UP-' correspond to prokaryotic sequences. Sequences from MMETSP

1540 are colored in black. Blue and orange clades represent the sequences corresponding to the

Creolimax fragrantissima and Sphaeroforma arctica EUKNR and NAD(P)H-NIR, respectively.

Supplementary Fig 23. Maximum likelihood phylogenetic tree inferred from eukaryotic NRT2, with

some prokaryotic sequences used as outgroup and excluding sequences from Labyrinthulea and

1545 Teretosporea. The tree was rooted at the branch that separates the eukaryotic clade from the

bacterial sequences. Statistical support values (1000-replicates UFBoot) are shown in all nodes.

Eukaryotic sequence names are abbreviated with the four-letter code (see Supplementary Table 1)

and colored according to their major taxonomic group (see panel). All sequences starting with 'UP-'

correspond to prokaryotic sequences.

1550

Supplementary Fig 24. Maximum likelihood phylogenetic tree inferred from eukaryotic NAD(P)H-

NIR, with some prokaryotic sequences used as outgroup and excluding sequences from

Labyrinthulea and Teretosporea. The tree was rooted in the branch that separates the eukaryotic

clade from the bacterial sequences, with nodes. Statistical support values (1000-replicates UFBoot)

1555 are shown for all nodes. Eukaryotic sequence names are abbreviated with the four-letter code (see

Supplementary Table 1) and colored according to their major taxonomic group (see panel). All

sequences starting with 'UP-' correspond to prokaryotic sequences.

Supplementary Fig 25. Unrooted representation of a maximum likelihood phylogenetic tree inferred

1560 from eukaryotic (mitochondrial protein) and prokaryotic 'Cytochrome c oxidase subunit III' amino acid

sequences. Prokaryotic sequences are colored according to the corresponding phylum or class,

while eukaryotes are colored according to whether they contain or not a plastid/plastid-related

organelle (see panel). As expected, Alphaproteobacteria is the sister group to eukaryotes,

suggesting that the taxonomic representation of prok_db allow to detect proteins with signatures of

1565 Alphaproteobacteria, and hence of putative mitochondrial origin. The process of phylogenetic

inference and taxonomic assignation is explained in Materials and methods section.

Supplementary Fig 26. Unrooted representation of a maximum likelihood phylogenetic tree inferred

from eukaryotic (mitochondrial protein) and prokaryotic 'Cytochrome b' amino acid sequences.

1570 Prokaryotic sequences are colored according to the corresponding phylum or class, while eukaryotes

are colored according to whether they contain or not a plastid/plastid-related organelle (see panel).

As expected, Alphaproteobacteria is the sister group to eukaryotes, suggesting that the taxonomic

representation of prok_db allow to detect proteins with signatures of Alphaproteobacteria, and hence

of putative mitochondrial origin. The process of phylogenetic inference and taxonomic assignation is

1575 explained in Materials and methods section.

Supplementary Fig 27. Maximum likelihood phylogenetic tree of TPmet proteins (selected from the

blue clade in Supplementary Fig 19), with some prokaryotic sequences used as outgroup (see

Materials and methods section). Eukaryotic sequence names are abbreviated with the four-letter

1580 code (see Supplementary Table 1) and colored according to their major taxonomic group (see panel).

All sequences starting with 'UP-' correspond to prokaryotic sequences. A third and last phylogenetic

tree was constructed using sequences from the blue clades (see Supplementary Fig 20).

bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 1 available under aCC-BY-NC 4.0 International license.

other aminoacids and metabolites

GS Gln EUKNR GOGAT

EUKNR Glu - NRT2 - - + NO3 NO3 NO2 NH4

NAD(P)H-NIR

or GDH

2-OG Fd-NIR

chloroplast bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 2 available under aCC-BY-NC 4.0 International license.

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nrt2 euknr Archaeplastida SAR Opisthokonta NAD(P)H-nir Rhodophyta Rhizaria Holozoa Fd-nir Chlorarachniophyta Teretosporea Chloroplastida present and Alveolata Ichthyosporea in cluster Streptophyta present but not Myzozoa Holomycota in cluster Chlorophyta Stramenopiles Fungi Others Autotrophs Labyrinthulea Glaucophyta Fungal-like Ochrophyta Amoebozoa Cryptophyta osmotrophs Oomycota Haptophyta bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 3 available under aCC-BY-NC 4.0 International license.

Fd-NIR NAD[P]H-NIR

Eukaryotes

NRT2 Eukaryotes Taxonomy Bacteria Cytophaga-Flexibacter-Bacteroides Planctomycetes Aquiﬁcaeota Cyanobacteria [Plastid donors] Alphaproteobacteria [Mitochondrial donors] Betaproteobacteria Gammaproteobacteria Others Archaea Euryarchaeotas Eukaryota Taxa with plastid/plastid-related organelles Other eukaryotes bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 4 available under aCC-BY-NC 4.0 International license.

Bact SUOX Euk SUOX EUKNR Euk NADH red

B Oxidored_molyb Mo-co_dimer Cyt-b5 FAD_binding_6 NAD_binding_1

C Bact Cyt-b5 prot Bact Cyt-b5 Euk Cyt-b5 Crei/Anid EUKNR Euk Cyt-b5 prot

4.63e-025 1.73e-018 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 5 available under aCC-BY-NC 4.0 International license.

A. anophagefferens (Ochrophyta) NAD[P]H-NIR Fd-NIR 89 E. huxleyi 82 Chrysochromulina sp. Fungi 80 100 T. oceanica (Ochrophyta) 100 71 G. prolifera (Fungi) T. pseudonana (Ochrophyta) 100 100 P. tricornutum (Ochrophyta) 57 C. limacisporum (Teretosporea) N. gaditana (Ochrophyta) 61 S. punctatus (Fungi) 80 91 E. siliculosus (Ochrophyta) Oomycota 81 B. natans (Chlorarachniophyta) 100 62 V. carteri (Chlorophyta) 100 C. fragrantissima (Ichthyosporea, Teretosporea) 94 100 C. reinhardtii (Chlorophyta) 100 100 S. arctica (Ichthyosporea, Teretosporea) C. variabilis (Chlorophyta) 93 62 C. crispus 55 Labyrinthulea 100 98 P. yezoensis 16 C. paradoxa (Glaucophyta) Ochrophyta 100 G. theta (Cryptophyta) M. pusila (Chlorophyta) 100 100 100 Myzozoa O. tauri (Chlorophyta) 94 Embryophyta 97 Bacteria 86 G. sulphuraria 0.1 Bacteria Fungi 100 99 0.1 92 C. limacisporum (Teretosporea)

NRT2 100 Labyrinthulea 100 73 EUKNR Oomycota Bootstrap colors 88 C. merolae

100 <90 UFBoot C. paradoxa (Glaucophyta) C. fragrantissima (Ichthyosporea, Teretosporea) 100 B.natans (Chlorarachniophyta) 97 100 S. arctica (Ichthyosporea, Teretosporea) 90-94 UFBoot C. variabilis (Chlorophyta) 95-100 UFBoot 97 Ochrophyta 25 97 100 C. reinhardtii (Chlorophyta) 94

100 99 V. carteri (Chlorophyta) 94 B. natans (Chlorarachniophyta) Taxonomy 98 100 83 100 100 Haptophyta Oomycota 62 100 A. anophagefferens (Ochrophyta) Rhodophyta 100 99 Chloroplastida 95 S. arctica (Ichthyosporea, Teretosporea) 100 94 Myzozoa Rhizaria 100 C. fragrantissima (Ichthyosporea, Teretosporea) 100 Alveolata

Stramenopiles 100 99 G. prolifera (Fungi) 100 Amoebozoa S. punctatus 99 90 G. theta (Cryptophyta) Sulfite oxidases A.castellanii Holozoa (Fungi) Holomycota 100 89 Others A. oryzae (Fungi) 100 A. nidulans (Fungi) 100

C. paradoxa (Glaucophyta) 100 1

100 Bacteria

1 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 6 available under aCC-BY-NC 4.0 International license.

A P. infestans (Oomycota, Stramenopiles) Pfam protein domains NRT2 NRT2 NRT2 EUKNR NAD(P)H-NIR Major Facilitator Superfamily

Oxidoreductase molybdopterin binding Mo-co oxidoreductase dimerisation

Cytochrome b5-like Heme/Steroid binding S. arctica (Ichthyosporea, Holozoa) FAD binding CS-pNR NAD(P)H-NIR NAD-binding NRT2

Pyridine nucleotide-disulphide oxidoreductase

BFD-like [2Fe-2S] binding

Nitrite/Sulﬁte reductase ferredoxin-like half C. fragrantissima (Ichthyosporea, Holozoa) Nitrite and sulphite reductase 4Fe-4S CS-pNR Rieske-like [2Fe-2S] TPmet NRT2 NAD(P)H-NIR

Tetrapyrrole (Corrin/Porphyrin) Methylases

B CS-pNR, N-terminal region CS-pNR, C-terminal region

Other NAD[P]H-NIR Other EUKNR

100 Oomycota NAD[P]H-NIR Oomycota EUKNR 100 100 S. arctica CS-pNR, C-ter 95 100 S. arctica CS-pNR, N-ter C. fragrantissima CS-pNR, C-ter 100 C. fragrantissima CS-pNR, N-ter 100 S. arctica NAD[P]H-NIR 100 Tree scale: 0.1 C. fragrantissima NAD[P]H-NIR Tree scale: 0.1

C Origin of CS-pNR Replacement of the C-terminal region of EUKNR S. arctica by the N-terminal region of NAD(P)H-NIR C. fragrantissima EUKNR NAD(P)H-NIR CS-pNR NAD(P)H-NIR bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 7 available under aCC-BY-NC 4.0 International license.

A Marine Broth mL1 mL1 + NaNO3 mL1+ (NH4)2SO4 mL1 + urea 2 hours 2 72 hours 72 168 hours 168

B 500 Gene CS-pnr NAD(P)H-nir 400 nrt2

300 100

50 Relative mRNA abundance mRNA Relative

0 0 h 6 h 12 h 24 h 6 h 12 h 24 h 6 h 12 h 24 h 6 h 12 h 24 h Time

mL1 mL1+ NaNO3 mL1 + (NH4)2SO4 mL1 + urea Condition bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Figure 8 available under aCC-BY-NC 4.0 International license.

A . castellanii Other amoebozoans P. biforma T. trahens Other holozoans C . limacisporum C . perkinsii Fungi S . destruens A . whisleri P. gemmata I. hoferi A . parasiticum C . fragrantissima S . arctica F. alba P. atlantis R . allomyces Microsporidia A . macrogynus Labyrinthulea C . anguillulae P iromyces sp. G. prolifera S . punctatus B . dendrobatidis C . coronatus C . reversa U. ramanniana P. blakesleeanus R . oryzae M. circinelloides R . irregularis M. verticillata U. maydis C . cinerea C . neoformans S . pombe Other ascomycetes / Chlorophyta B . adeninivorans Ochrophyta S . cerevisiae O. parapolymorpha Archaeplastida B . natans Possible Archaeplastida donor P. brassicae Planctomycetes (Bacteria) R . filosa C iliophora S . minutum P. marinus V. brassicaformis Apicomplexa B . hominis Labyrinthulea * Other ochrophytes * Possible N. gaditana Archaeplastida donor E . siliculosus A . astaci S . parasitica A . laibachii P. ultimum H. arabidopsidis Bacteria (uncertain phyla) Ichthyosporea P. infestans Eukaryotic origin P. halstedii Cyanobacteria (Bacteria) Possible G. theta Rhodophyta donor C . paradoxa Streptophyta * Chlorophyta Chloroplastida C . merolae Unknown donor G. sulphuraria Ochrophyta P. yezoensis C . crispus E . huxleyi Chrysochromulina sp. N. longa E xcavata

nrt2 euknr Archaeplastida SAR Opisthokonta NAD(P)H-nir Rhizaria Holozoa Fd-nir Rhodophyta Chlorarachniophyta Teretosporea present and Chloroplastida Alveolata Ichthyosporea in cluster Streptophyta present but not Myzozoa Holomycota in cluster Chlorophyta Stramenopiles Fungi Transfer of Others Labyrinthulea NAP cluster Glaucophyta Ochrophyta Amoebozoa Single NAP Cryptophyta gene transfer Oomycota Haptophyta Pathway loss bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgureavailable 1 under aCC-BY-NC 4.0 International license.

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nrt2 euknr Archaeplastida SAR Opisthokonta NAD(P)H-nir Rhodophyta Rhizaria Holozoa Fd-nir Chlorarachniophyta Teretosporea Chloroplastida present and Alveolata Ichthyosporea in cluster Streptophyta present but not Myzozoa Holomycota in cluster Chlorophyta Stramenopiles Fungi Complete Others Labyrinthulea pathway Glaucophyta Ochrophyta Amoebozoa Partial Cryptophyta pathway Oomycota Haptophyta bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure available2 under aCC-BY-NC 4.0 International license.

A) Correlation between NAPs distribution in the whole dataset

nrt2 nr nir-fd nir-NAD(P)H 100% nrt2 1.00 0.94 0.82 0.84 nr 0.94 1.00 0.82 0.85 nir-fd 0.82 0.82 1.00 0.73 nir-NAD(P)H 0.84 0.85 0.73 1.00

B) Correlation between NAPs distribution, considering only taxa with at least 1 NAP nrt2 euknr Fd-nir NAD(P)H-nir nrt2 1.00 0.81 0.49 0.53 euknr 0.81 1.00 0.47 0.58 Fd-nir 0.49 0.47 1.00 0.22 NAD(P)H-nir 0.53 0.58 0.22 1.00

C) Correlation between NAPs distribution and the diﬀerent nutrient acquisition strategies

nrt2 euknr Fd-nir NAD(P)H-nir Autotrophs (70) 0.97 0.90 0.87 0.23

Phagotrophs (65) 0.00 0.02 0.00 0.00

Fungi (31) 0.47 0.50 0.00 0.47

Teretosporea (9) 0.33 0.33 0.00 0.33

Oomycota (7) 0.71 0.29 0.00 0.29

Fungi-like Labyrinthulea (3) 1.00 0.00 1.00 osmotrophs 1.00

Non-autotrophs Others (26) 0.00 0.00 0.00 0.00 0% bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure available3 under aCC-BY-NC 4.0 International license.

UP000019772_2530_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sabinae 100 100 UP000029507_2333_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_stellifer 95 UP000033163_3265_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_riograndensis UP000006868_2181 96 100 UP000003981_2598_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sp_oral_taxon_786 100 UP000034827_3265_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sp_DMB20 UP000003900_209_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_dendritiformis 100 100 UP000006321_4161_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_alvei UP000029431_28_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_larvae 100 UP000003445_5515 98 UP000017118_2939_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_saccharobutylicum 50 63 UP000005106_3086_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_DL-VIII 100 UP000001325_2772_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_Maddingley_MBC34-26 35 100 UP000000565_2921_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_rubrum UP000005435_1940_phylum_low_GC_Gram+/class_Clostridia/sp_[Clostridium]_clariflavum UP000037269_4522_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_migulanus 73 78 UP000007279_4811_phylum_low_GC_Gram+/class_Firmibacteria/sp_- UP000037969_2629_phylum_low_GC_Gram+/class_Firmibacteria/sp_Thermoactinomyces_vulgaris 82 85 UP000033488_1991_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridiaceae_bacterium_c20a UP000005850_2720_phylum_low_GC_Gram+/class_Firmibacteria/sp_Brevibacillus_laterosporus UP000001384_607_phylum_low_GC_Gram+/class_Firmibacteria/sp_- 100 100UP000001417_4026 100 UP000000594_3037_phylum_low_GC_Gram+/class_Firmibacteria/sp_anthrax_bacterium UP000006654_1102_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_medusa 100 93 86 UP000002300_1081_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_cytotoxis UP000037908_2709_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_CHD6a 100 84 99 UP000017805_3031 UP000001401_3999_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_cellulosilyticus 45 UP000004046_3906_phylum_low_GC_Gram+/class_Firmibacteria/sp_Desmospora_sp_8437 UP000023566_3167_phylum_low_GC_Gram+/class_Firmibacteria/sp_Geobacillus_thermophilus 99 100 100 UP000002386_1094_phylum_low_GC_Gram+/class_Firmibacteria/sp_- UP000027602_1257_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_methanolicus 64 100 UP000013300_1268_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_1NLA3E 95 UP000007271_672_phylum_low_GC_Gram+/class_Firmibacteria/sp_Lactobacillus_coryniformis 98 UP000036353_991_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_smithii UP000008937_321_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_SY8519 75 74 UP000005139_2375_phylum_low_GC_Gram+/class_Negativicutes/sp_Thermosinus_carboxydivorans UP000027983_3777_phylum_low_GC_Gram+/class_Negativicutes/sp_Pelosinus_lilaceae UP000000787_4353_phylum_green_nonsulfur_bacteria/class_Chloroflexus/Deinococcus_group/sp_Herpetosiphon_giganteus UP000003955_3247_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sp_Tu6071 100 72 UP000002779_3865_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sp_SPB74_2 68 UP000032413_2131_phylum_actinobacteria/class_high_GC_Gram+/sp_- UP000002357_2416_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_clavuligerus 62 UP000037991_1714_phylum_actinobacteria/class_high_GC_Gram+/sp_Actinobacteria_bacterium_OK074 90 UP000008043_2717_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_davawensis 65 82 UP000037758_7507_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sp_AS58 UP000037741_6992_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sp_MMG1533 74 UP000032234_4080_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_cyaneogriseus_2 UP000017984_8425_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_roseochromogenus 71 71 99 71 UP000031501_962_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 94 UP000007170_7935 100 UP000036399_3626_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sp_PBH53_1 UP000029482_6219_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_glaucescens 100 UP000003824_356 58 100 42 UP000002968_3505_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_griseoflavus 98 UP000001973_1983 59 UP000037773_5626 UP000008703_2155_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_violaceusniger_2 93 60 UP000000377_5191_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_bingchenggensis_2 UP000004217_5380_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_zinciresistens UP000002785_1713_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sviceus 100 100 UP000033641_984_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sp_WM6386 UP000001397_5423_2 UP000007113_146_phylum_Fibrobacteres/Acidobacteria_group/class_Acidobacteriia/sp_Granulicella_mallensis_1 100 99 99 100 UP000006844_2253_phylum_Fibrobacteres/Acidobacteria_group/class_Acidobacteriia/sp_Terriglobus_saanensis 98 UP000002432_2401_phylum_Fibrobacteres/Acidobacteria_group/class_Acidobacteriia/sp_Koribacter_versatilis UP000008915_377_phylum_low_GC_Gram+/class_Clostridia/sp_Thermaerobacter_marianensis_1 100 92 UP000004221_1769_phylum_green_nonsulfur_bacteria/class_Thermomicrobia/sp_strain_Lb_2 UP000027982_625_phylum_Armatimonadetes/class_Fimbriimonadia/sp_Fimbriimonas_ginsengisoli 67 100 UP000014227_389_phylum_Armatimonadetes/class_Chthonomonadetes/sp_Chthonomonas_calidirosea_2 UP000005824_1533_phylum_verrucomicrobia/class_Xiphinematobacteriaceae/sp_Chthoniobacter_flavus_1 UP000001169_833_phylum_euryarchaeotes/class_Halomebacteria/sp_Halobacterium_marismortui 99 96 UP000001746_788_phylum_euryarchaeotes/class_Halomebacteria/sp_Halomicrobium_mukohataei 96 UP000004595_975_phylum_euryarchaeotes/class_Halomebacteria/sp_Halobacterium_sp_DL1 90 UP000008243_1141_phylum_euryarchaeotes/class_Halomebacteria/sp_Haloferax_volcanii 96 UP000001975_222_phylum_euryarchaeotes/class_Halomebacteria/sp_Haloquadratum_walsbyi 100 100 100 UP000000740_2637_phylum_euryarchaeotes/class_Halomebacteria/sp_Halorubrum_lacusprofundi UP000006663_255_phylum_euryarchaeotes/class_Halomebacteria/sp_Halogeometricum_borinquense 100 UP000000390_516_phylum_euryarchaeotes/class_Halomebacteria/sp_Halalkalicoccus_jeotgali UP000000740_484 100 UP000006637_2175_phylum_actinobacteria/class_Rubrobacteridae/sp_Rubrobacter_xylanophilus 100 100 UP000025229_621_phylum_actinobacteria/class_Rubrobacteridae/sp_Rubrobacter_radiotolerans 100 UP000000323_270_phylum_-/class_-/sp_Thermobaculum_terrenum UP000003688_3335_phylum_verrucomicrobia/class_Verrucomicrobiae/sp_Pedosphaera_parvula 100 93 UP000031643_2858_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methyloceanus_cenitepidus UP000000787_1315 UP000002574_1105_phylum_Aquificaeota/class_Aquificae/sp_Hydrogenobacter_thermophilus 100 99 100 UP000001201_334_phylum_Aquificaeota/class_Aquificae/sp_Sulfurihydrogenibium_sp_YO3AOP1 100 UP000002043_525_phylum_Aquificaeota/class_Aquificae/sp_Thermocrinis_albus UP000005981_109_phylum_Aquificaeota/class_Aquificae/sp_Hydrogenivirga_sp_128-5-R1-1 100 66 UP000000798_187_phylum_Aquificaeota/class_Aquificae/sp_Aquifex_aeolicus UP000001660_2067_phylum_Thermodesulfovibrio_group/class_Nitrospiria/sp_Nitrospira_defluvii UP000017396_198_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_kilaueensis 100 UP000000557_2817_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_violaceus UP000010101_3303_phylum_cyanophytes/class_-/sp_- 100 75 UP000010474_1007_phylum_cyanophytes/class_-/sp_Anabaena_cylindrica 65 UP000010475_2899_phylum_cyanophytes/class_-/sp_Cylindrospermum_stagnale 70 UP000001191_2321_phylum_cyanophytes/class_-/sp_Nostoc_punctiforme UP000010390_2429_phylum_cyanophytes/class_-/sp_Calothrix_sp_PCC7507 64 UP000019325_1417_phylum_cyanophytes/class_-/sp_Nodularia_spumigena 87 UP000010381_2265_phylum_cyanophytes/class_-/sp_Nostoc_sp_PCC_7107 87 69 UP000010378_4492_phylum_cyanophytes/class_-/sp_- 100 UP000002483_187 88 UP000004344_487_phylum_cyanophytes/class_-/sp_- UP000010477_921_phylum_cyanophytes/class_-/sp_Calothrix_parietina 89 55 UP000010384_3421_phylum_cyanophytes/class_-/sp_Croococcidiopsis_thermalis 64 UP000010476_2388_phylum_cyanophytes/class_-/sp_Chroococcus_sp_Cey_un UP000010471_297_phylum_cyanophytes/class_-/sp_Oscillatoria_sp_Mc UP000001938_2801_phylum_cyanophytes/class_-/sp_Cyanobacteria_sp_Yellowstone_B-Prime 100 99 UP000010385_475_phylum_cyanophytes/class_-/sp_Synechococcus_sp_Rippka_B2 76 UP000010383_271_phylum_cyanophytes/class_-/sp_Geitlerinema_sp_PCC_7407 UP000001332_4247_phylum_cyanophytes/class_-/sp_Oscillatoriales_cyanobacterium_JSC-12 83 81 83 UP000010386_1786_phylum_cyanophytes/class_-/sp_Pseudanabaena_sp_PCC7367 92 UP000010472_3518_phylum_cyanophytes/class_-/sp_Crinalium_epipsammum 87 UP000000268_6633_phylum_cyanophytes/class_-/sp_- UP000010478_4726_phylum_cyanophytes/class_-/sp_Oscillatoria_nigroviridis 100 UP000004532_2649_phylum_cyanophytes/class_-/sp_- 54 UP000010366_4344_phylum_cyanophytes/class_-/sp_Sphaerogonium_minutum 100 35 35 UP000027395_2048_phylum_cyanophytes/class_-/sp_- 59 UP000000737_1157_phylum_cyanophytes/class_-/sp_Lyngbya_sp_PCC_8106 UP000008878_3432_phylum_cyanophytes/class_-/sp_Trichodesmium_erythraeum UP000002384_1491_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7424 100 UP000008206_3750_phylum_cyanophytes/class_-/sp_Cyanothece_sp_PCC_7822 74 UP000003835_7502_phylum_cyanophytes/class_-/sp_Microcoleus_chthonoplastes 100 UP000006803_1752_phylum_cyanophytes/class_-/sp_- 84 100 UP000001688_3078_phylum_cyanophytes/class_-/sp_- 100 UP000010389_2710_phylum_cyanophytes/class_-/sp_Leptolyngbya_sp_PCC_7376 97 UP000010483_1170_phylum_cyanophytes/class_-/sp_Cyanobacterium_stanieri 86 100 UP000010480_118_phylum_cyanophytes/class_-/sp_Cyanobacterium_aponinum UP000034681_2334_phylum_cyanophytes/class_-/sp_Prochlorothrix_hollandica 50 89 89 UP000005766_3305_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7335 UP000010481_217_phylum_cyanophytes/class_-/sp_Aphanothece_halophytica_'Solar_Lake' 89 52 UP000010380_633_phylum_cyanophytes/class_-/sp_Rivularia_sp_LIP UP000001203_2287 100 76 29 UP000003922_3071_phylum_cyanophytes/class_-/sp_Erythrosphaera_marina UP000010473_1567_phylum_cyanophytes/class_-/sp_Stanieria_cyanosphaera 76 UP000008204_3295_phylum_cyanophytes/class_-/sp_- 74 UP000010382_649_phylum_cyanophytes/class_-/sp_Pleurocapsa_minor 77 90 UP000001510_5218_phylum_cyanophytes/class_-/sp_Microcystis_aeruginosa UP000003959_5969_phylum_cyanophytes/class_-/sp_Moorea_producta UP000010367_5533_phylum_cyanophytes/class_-/sp_Phormidium_acuminatum UP000001425_2420_phylum_cyanophytes/class_-/sp_- 95 100 100 UP000010379_1198_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_6312 Taxonomy 86 UP000000440_1158_phylum_cyanophytes/class_-/sp_- Alignment statistics UP000002511_390_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7425 UP000010471_24 100 UP000010384_5459 Bacteria UP000001566_2386 86 UP000001422_123 Number of taxa: 190 69 86 Cytophaga-Flexibacter-Bacteroides UP000004972_1728_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RS9916 93 85 UP000005593_224 100 UP000001423_879 Planctomycetes 100 UP000002535_834 Alignment length: 444 UP000001115_2391_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RCC307 100 Aquiﬁcaeota UP000003950_337_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7001 99 62 100 UP000010388_2505_phylum_cyanophytes/class_-/sp_Cyanobium_gracile UP000002935_196_phylum_cyanophytes/class_-/sp_Synechococcus_sp_SYN Cyanobacteria [Plastid donors] Parsimony info. sites: 93.90% UP000002717_79 Tpse_XP_002289265 100 Alphaproteobacteria [Mitochondrial donors] 100 Toce_15700 68 Ptri_XP_002180496 Missing data: 0.61% 67 Ehux_428968 Betaproteobacteria 100 Chsp_2401 96 tBLASTn_Aano_scaffold_5_95839-97332_frame3 71 Ngad_10682 Gammaproteobacteria 45 Bnat_50588 Gsul_5197 Others Crei_XP_001696787 74 100 100 Vcar_XP_002955216 72 Cvar_EFN52613 Phylogenetic inference 99 75 Esil_CBJ25514 Archaea Pyez_1166_g159 100 Ccri_T00003048001 Cpar_20981Contig26815 Euryarchaeotas Maximium likelihood Ntab_919 100 Ntab_1822 100 Ntab_2612 100 100 Ntab_464 Eukaryota 99 Acoe_015_00061 1000 UFBoot replicates 100 100 Mgut_mgv1a003340m Taxa with plastid/plastid-related organelles 100 Atha_10060 Bdis_3g57990 87 100 Sbic_04g034160 Other eukaryotes LG+R8 Smoe_XP_002987413 91 Ppat_XP_001777025 100 93 97 Ppat_XP_001775824 Kfla_2615 100 Gthe_81582 Otau_XP_003081527 100 Mpus_Micpu70828

0.3 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure available4 under aCC-BY-NC 4.0 International license.

UP000010483_2088_phylum_cyanophytes/class_-/sp_Cyanobacterium_stanieri 100 58 UP000010480_93_phylum_cyanophytes/class_-/sp_Cyanobacterium_aponinum UP000008204_2062_phylum_cyanophytes/class_-/sp_- 74 UP000001405_585_phylum_cyanophytes/class_-/sp_cyanobacterium_UCYN-A 100 97 UP000003922_5578_phylum_cyanophytes/class_-/sp_Erythrosphaera_marina 71 UP000001203_2566 UP000008206_2026_phylum_cyanophytes/class_-/sp_Cyanothece_sp_PCC_7822 100 UP000002384_164_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7424 61 99 UP000010473_314_phylum_cyanophytes/class_-/sp_Stanieria_cyanosphaera Alignment statistics 72 UP000001425_64_phylum_cyanophytes/class_-/sp_- UP000001510_4695_phylum_cyanophytes/class_-/sp_Microcystis_aeruginosa 75 78 UP000010382_393_phylum_cyanophytes/class_-/sp_Pleurocapsa_minor UP000001688_569_phylum_cyanophytes/class_-/sp_- 100 Number of taxa: 108 44 47 UP000010389_2752_phylum_cyanophytes/class_-/sp_Leptolyngbya_sp_PCC_7376 32 UP000010481_1229_phylum_cyanophytes/class_-/sp_Aphanothece_halophytica_'Solar_Lake' UP000010477_4305_phylum_cyanophytes/class_-/sp_Calothrix_parietina 47 UP000000268_5089_phylum_cyanophytes/class_-/sp_- Alignment length: 144 UP000010366_4045_phylum_cyanophytes/class_-/sp_Sphaerogonium_minutum UP000001191_4153_phylum_cyanophytes/class_-/sp_Nostoc_punctiforme 96 UP000010381_1020_phylum_cyanophytes/class_-/sp_Nostoc_sp_PCC_7107 96 UP000002483_121 100 Taxonomy 61 UP000010378_1699_phylum_cyanophytes/class_-/sp_- Parsimony info. sites: 86.80% 48 61 UP000010475_4609_phylum_cyanophytes/class_-/sp_Cylindrospermum_stagnale Bacteria UP000019325_574_phylum_cyanophytes/class_-/sp_Nodularia_spumigena Cytophaga-Flexibacter-Bacteroides 100 UP000001511_1358_phylum_cyanophytes/class_-/sp_Trichormus_azollae 94 UP000010474_732_phylum_cyanophytes/class_-/sp_Anabaena_cylindrica Planctomycetes Missing data: 19.30% 60 100 UP000010101_237_phylum_cyanophytes/class_-/sp_- 70 Aquiﬁcaeota 41 84 UP000010390_430_phylum_cyanophytes/class_-/sp_Calothrix_sp_PCC7507 UP000004344_3677_phylum_cyanophytes/class_-/sp_- Cyanobacteria [Plastid donors] 99 UP000010380_1874_phylum_cyanophytes/class_-/sp_Rivularia_sp_LIP Alphaproteobacteria [Mitochondrial donors] UP000010476_2020_phylum_cyanophytes/class_-/sp_Chroococcus_sp_Cey_un 86 Betaproteobacteria 67 UP000010384_1779_phylum_cyanophytes/class_-/sp_Croococcidiopsis_thermalis UP000010471_824_phylum_cyanophytes/class_-/sp_Oscillatoria_sp_Mc 99 Gammaproteobacteria UP000010472_1765_phylum_cyanophytes/class_-/sp_Crinalium_epipsammum Phylogenetic inference UP000000440_11_phylum_cyanophytes/class_-/sp_- Others 99 92 UP000010379_846_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_6312 UP000002511_3769_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7425 Archaea UP000033607_3216_phylum_cyanophytes/class_-/sp_Lyngbya_robusta 75 97 UP000000737_5765_phylum_cyanophytes/class_-/sp_Lyngbya_sp_PCC_8106 Euryarchaeotas Maximium likelihood 99 UP000006803_4646_phylum_cyanophytes/class_-/sp_- 63 69 UP000027395_3015_phylum_cyanophytes/class_-/sp_- Eukaryota UP000010478_437_phylum_cyanophytes/class_-/sp_Oscillatoria_nigroviridis 69 100 Taxa with plastid/plastid-related organelles UP000004532_2306_phylum_cyanophytes/class_-/sp_- 1000 UFBoot replicates 93 UP000008878_2981_phylum_cyanophytes/class_-/sp_Trichodesmium_erythraeum Other eukaryotes UP000003959_4761_phylum_cyanophytes/class_-/sp_Moorea_producta 79 UP000003835_1742_phylum_cyanophytes/class_-/sp_Microcoleus_chthonoplastes UP000001566_1773 96 LG+R4 97 UP000005593_989 UP000004972_2343_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RS9916 62 100 98 UP000001422_732 UP000001115_676_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RCC307 99 UP000003950_2048_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7001 97 100 UP000002935_1563_phylum_cyanophytes/class_-/sp_Synechococcus_sp_SYN UP000010388_3017_phylum_cyanophytes/class_-/sp_Cyanobium_gracile 99 UP000001420_1744_phylum_cyanophytes/class_-/sp_- 100 100 UP000000788_1706_phylum_cyanophytes/class_-/sp_Prochlorococcus_maritima 100 UP000001026_1513 99 100 UP000002535_352 85 UP000001423_1682 UP000002717_1278 89 53 UP000034681_3566_phylum_cyanophytes/class_-/sp_Prochlorothrix_hollandica UP000010367_1146_phylum_cyanophytes/class_-/sp_Phormidium_acuminatum 70 78 UP000005766_4071_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7335 82 UP000010383_1114_phylum_cyanophytes/class_-/sp_Geitlerinema_sp_PCC_7407 UP000001332_1807_phylum_cyanophytes/class_-/sp_Oscillatoriales_cyanobacterium_JSC-12 UP000001332_319 93 100 100 UP000010382_2060 99 UP000005766_2972 100 UP000010384_2360 UP000004344_29 99 93 UP000010390_440 UP000000557_1686_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_violaceus 100 94 UP000017396_3029_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_kilaueensis UP000001938_332_phylum_cyanophytes/class_-/sp_Cyanobacteria_sp_Yellowstone_B-Prime UP000010386_361_phylum_cyanophytes/class_-/sp_Pseudanabaena_sp_PCC7367 99 UP000010385_2640_phylum_cyanophytes/class_-/sp_Synechococcus_sp_Rippka_B2 Ppat_XP_001765875 98 78 Ppat_XP_001782922 99 Ppat_XP_001770075 100 Ppat_XP_001755730 98 Mpol_1429 Smoe_XP_002983887 100 Smoe_XP_002960780 97 Mgut_mgv1a013112m 73 73 Acoe_118_00037 77 100 Atha_7190 Sbic_01g006370 100 Bdis_1g06890 84 Kfla_12539 Crei_XP_001696798 100 100 Vcar_XP_002952500 96 82 Cvar_EFN58854 Otau_XP_003078706 100 46 Mpus_Micpu26202 Aano_F0YGY1 57 Bnat_54026 Cmer_CMV201C 67 Smin_025464_t1 95 100Smin_025465_t1 73 Smin_012847_t1 55 Vbra_9324 Toce_14761 100 100 Tpse_XP_002297523 93 76 Ptri_YP_874361 99 Ngad_9076 Esil_CAT18840 Cpar_photosyst2subU3 95 Gsul_3743

0.2 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which Supplementarywas not certified by peer ﬁ review)gure is the author/funder,5 who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license.

UP000008961_1324_phylum_low_GC_Gram+/class_Clostridia/sp_butyrate-producing_bacterium_SS3/4 96 95UP000018268_1307_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 95UP000018009_4051_phylum_low_GC_Gram+/class_Clostridia/sp_- 95UP000001662_1624_phylum_low_GC_Gram+/class_Clostridia/sp_[Clostridium]_saccharolyticum UP000008797_2999_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_M62/1 UP000006599_2145_phylum_low_GC_Gram+/class_Clostridia/sp_Lachnospiraceae_bacterium_ICM7 8084 95UP000018263_2533_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 17UP000018246_801_phylum_low_GC_Gram+/class_Clostridia/sp_Hungatella_hathewayi 9117UP000002970_3310_phylum_low_GC_Gram+/class_Clostridia/sp_- UP000017929_352_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 66 UP000005384_621 UP000018177_1558_phylum_low_GC_Gram+/class_Clostridia/sp_Blautia_sp_MGS 97 67UP000018386_881_phylum_low_GC_Gram+/class_-/sp_Firmicutes_bacterium_MGS UP000006000_2061_phylum_low_GC_Gram+/class_Clostridia/sp_[Eubacterium]_ventriosum 36 46 UP000017939_442_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS UP000018124_94_phylum_low_GC_Gram+/class_Clostridia/sp_Eubacterium_sp_MGS 88 UP000017928_224_phylum_low_GC_Gram+/class_-/sp_Firmicutes_bacterium_MGS 33 35UP000018207_1063_phylum_low_GC_Gram+/class_-/sp_Firmicutes_bacterium_MGS 68UP000003336_5711_phylum_low_GC_Gram+/class_Clostridia/sp_Eisenbergiella_tayi 76UP000017963_877_phylum_low_GC_Gram+/class_-/sp_Firmicutes_bacterium_MGS 74 82 UP000003011_1549_phylum_low_GC_Gram+/class_Clostridia/sp_Johnsonella_ignava UP000017986_680_phylum_low_GC_Gram+/class_Clostridia/sp_Streptococcus_hansenii 76 59UP000018378_959_phylum_low_GC_Gram+/class_Clostridia/sp_[Eubacterium]_ramulus UP000008798_1103_phylum_low_GC_Gram+/class_Clostridia/sp_Coprococcus_catus UP000018022_964_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 76 UP000018242_1182_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 30 UP000002294_50_phylum_low_GC_Gram+/class_Tissierellia/sp_Peptostreptococcus_prevotii 92 99UP000018002_1764_phylum_low_GC_Gram+/class_Clostridia/sp_Coprococcus_sp_MGS 99UP000017949_1476_phylum_low_GC_Gram+/class_Clostridia/sp_Coprococcus_eutactus UP000018342_1153_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 69 86UP000018032_2018_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 13 100UP000018071_631_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 96 UP000017961_1373_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS UP000018281_2597_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS UP000018023_1701_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 97 96 96UP000018137_714_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS UP000018292_1712_phylum_low_GC_Gram+/class_Clostridia/sp_Roseburia_sp_MGS 35 UP000008467_4074_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_lentocellum UP000008234_1408_phylum_low_GC_Gram+/class_Clostridia/sp_Mageeibacillus_indolicus 38 99 UP000017904_457_phylum_low_GC_Gram+/class_Clostridia/sp_Eubacterium_sp_MGS UP000005435_811_phylum_low_GC_Gram+/class_Clostridia/sp_[Clostridium]_clariflavum 97 UP000011220_2024_phylum_low_GC_Gram+/class_Clostridia/sp_[Clostridium]_stercorarium UP000003821_677_phylum_low_GC_Gram+/class_Tissierellia/sp_Peptostreptococcus_vaginalis 100 14 69 UP000005277_465_phylum_low_GC_Gram+/class_Tissierellia/sp_Peptostreptococcus_hydrogenalis 67 Smin_009383_t1 UP000031386_657_phylum_low_GC_Gram+/class_Tissierellia/sp_Streptococcus_micros 14 UP000018161_862_phylum_low_GC_Gram+/class_-/sp_Firmicutes_bacterium_MGS 98 100 UP000018256_554_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Corallococcus_sp_MGS 6714 98 UP000018132_1193_phylum_low_GC_Gram+/class_Clostridia/sp_Faecalibacterium_sp_MGS UP000034076_1731_phylum_low_GC_Gram+/class_Clostridia/sp_Catabacter_hongkongensis UP000018041_918_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 88 UP000032801_92_phylum_low_GC_Gram+/class_Clostridia/sp_Paeniclostridium_sordellii 100 96UP000034407_1489_phylum_low_GC_Gram+/class_Clostridia/sp_Paraclostridium_benzoelyticum UP000005244_10_phylum_low_GC_Gram+/class_Clostridia/sp_Peptostreptococcaceae_bacterium_ACC19a 81 UP000035704_8_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_aceticum UP000000555_524_phylum_low_GC_Gram+/class_Clostridia/sp_Thermoanaerobacter_subterraneus 100 UP000002156_1871_phylum_low_GC_Gram+/class_Clostridia/sp_- 7694 UP000003680_1579_phylum_low_GC_Gram+/class_Tissierellia/sp_Peptoniphilus_sp_oral_taxon_375 100 UP000003705_640_phylum_low_GC_Gram+/class_Tissierellia/sp_Schleiferella_harei UP000002377_898_phylum_low_GC_Gram+/class_Clostridia/sp_- 88 UP000010797_375_phylum_low_GC_Gram+/class_Clostridia/sp_Desulfitobacterium_dichloroeliminans UP000004469_2783_phylum_low_GC_Gram+/class_Clostridia/sp_Eubacterium_sp_3_1_31 93 81UP000018179_3111_phylum_low_GC_Gram+/class_-/sp_- 90UP000018093_150_phylum_low_GC_Gram+/class_Erysipelotrichia/sp_[Eubacterium]_dolichum 90 UP000005950_118_phylum_low_GC_Gram+/class_Erysipelotrichia/sp_Holdemania_filiformis UP000004315_2433_phylum_low_GC_Gram+/class_Erysipelotrichia/sp_Pseudobacterium_biforme 79 91 UP000018332_975_phylum_low_GC_Gram+/class_-/sp_Firmicutes_bacterium_MGS UP000008801_519 100 85 UP000017945_1656_phylum_low_GC_Gram+/class_Erysipelotrichia/sp_Ristella_cylindroides UP000008963_1261_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_strain_SJ 94 99 UP000018274_2176_phylum_Spirochaetes/class_Spirochaetia/sp_Brachyspira_sp_MGS UP000003157_2873_phylum_low_GC_Gram+/class_Erysipelotrichia/sp_- UP000018000_608_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 94 100 100 UP000018401_143_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 100 UP000017955_831_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 69 100 UP000017930_1000_phylum_Tenericutes/class_mycoplasmas/sp_Acholeplasma_sp_MGS 97 UP000018014_1014_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_MGS UP000005707_2784_phylum_-/class_-/sp_Haloplasma_contractile UP000008308_4258_phylum_actinobacteria/class_high_GC_Gram+/sp_Verrucosispora_maris 100 100UP000037709_5166_phylum_actinobacteria/class_high_GC_Gram+/sp_Micromonospora_sp_NRRL_B-16802 97 UP000007882_581_phylum_actinobacteria/class_high_GC_Gram+/sp_Actinoplanes_missouriensis 86 98UP000000434_455_phylum_actinobacteria/class_high_GC_Gram+/sp_Thermonospora_fusca UP000002219_5000 100 100 UP000003779_3681_phylum_actinobacteria/class_high_GC_Gram+/sp_- UP000004367_2186_phylum_actinobacteria/class_high_GC_Gram+/sp_Mobilicoccus_pelagius 100 UP000033603_1835_phylum_actinobacteria/class_high_GC_Gram+/sp_Terrabacter_sp_28 100 UP000000439_528 83 100UP000007063_1265_phylum_actinobacteria/class_high_GC_Gram+/sp_- UP000003191_1475 61 99 100 UP000006173_187_phylum_actinobacteria/class_high_GC_Gram+/sp_strain_Ti 99 UP000008693_1022 UP000002019_555_phylum_Cloacimonetes/class_-/sp_Cloacimonas_acidaminovorans UP000001877_4847_phylum_low_GC_Gram+/class_Firmibacteria/sp_Brevibacillus_brevis 99 95 85 UP000006315_863_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_azotoformans 92 UP000001401_775_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_cellulosilyticus UP000007397_116_phylum_low_GC_Gram+/class_Firmibacteria/sp_Sporosarcina_halophila UP000004055_1175_phylum_low_GC_Gram+/class_Firmibacteria/sp_Staphylococcus_lugdunensis 56 93 92UP000008944_624_phylum_low_GC_Gram+/class_Firmibacteria/sp_Staphylococcus_pettenkoferi 99UP000007469_1860_phylum_low_GC_Gram+/class_Firmibacteria/sp_- 95 UP000000531_2285 UP000004465_171_phylum_low_GC_Gram+/class_Firmibacteria/sp_Facklamia_hominis UP000006443_1523_phylum_low_GC_Gram+/class_Clostridia/sp_Dethiobacter_alkaliphilus 54 UP000011765_1253_phylum_low_GC_Gram+/class_Clostridia/sp_Thermodesulfobium_narugense UP000000272_983_phylum_low_GC_Gram+/class_Clostridia/sp_Thermosediminibacter_oceani 99 82 UP000010802_261_phylum_low_GC_Gram+/class_Clostridia/sp_Tepidanaerobacter_acetatoxydans UP000001520_226_phylum_Deferribacteres/class_Flexistipes_group/sp_Deferribacter_desulfuricans UP000017985_1389_phylum_low_GC_Gram+/class_Negativicutes/sp_Dialister_sp_MGS 100 100UP000018365_1394_phylum_low_GC_Gram+/class_Negativicutes/sp_Dialister_sp_MGS 100UP000003277_1847_phylum_low_GC_Gram+/class_Negativicutes/sp_Dialister_succinatiphilus 100 UP000017966_253_phylum_low_GC_Gram+/class_Negativicutes/sp_Dialister_invisus 36 UP000003503_970_phylum_low_GC_Gram+/class_Negativicutes/sp_Dialister_microaerophilus UP000007968_1142_phylum_low_GC_Gram+/class_Negativicutes/sp_- 100 UP000018347_1603_phylum_low_GC_Gram+/class_Negativicutes/sp_Veillonella_seminalis 98 UP000003242_460_phylum_low_GC_Gram+/class_Negativicutes/sp_Megasphaera_sp_type_1 72 100 82 UP000010111_376_phylum_low_GC_Gram+/class_Negativicutes/sp_rumen_organism_LC 35 100UP000003195_298_phylum_low_GC_Gram+/class_Negativicutes/sp_Megasphaera_micronuciformis UP000005481_531_phylum_low_GC_Gram+/class_Negativicutes/sp_Anaeroglobus_geminatus UP000003240_1750_phylum_low_GC_Gram+/class_Negativicutes/sp_Acetonema_longum 94 99 UP000005139_1338_phylum_low_GC_Gram+/class_Negativicutes/sp_Thermosinus_carboxydivorans UP000003671_333_phylum_low_GC_Gram+/class_Negativicutes/sp_Mitsuokella_multiacidus 90 UP000003701_1225_phylum_low_GC_Gram+/class_Negativicutes/sp_Selenomonas_noxia 78 90 100UP000007887_626_phylum_low_GC_Gram+/class_Negativicutes/sp_- 61 UP000008806_486_phylum_low_GC_Gram+/class_Negativicutes/sp_Sphaerophorus_hypermegas 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UP000002207_1088_phylum_Fibrobacteres/Acidobacteria_group/class_Acidobacteriia/sp_Acidobacterium_capsulatum 100 92 100 UP000006844_1864_phylum_Fibrobacteres/Acidobacteria_group/class_Acidobacteriia/sp_Terriglobus_saanensis UP000006791_1622_phylum_Fibrobacteres/Acidobacteria_group/class_Blastocatellia/sp_strain_B 85 UP000007719_738_phylum_Dictyoglomus_group/class_Dictyoglomia/sp_Dictyoglomus_turgidus UP000001968_224_phylum_low_GC_Gram+/class_Clostridia/sp_Syntrophomonas_wolfei 100 87 100 UP000045545_820_phylum_low_GC_Gram+/class_Clostridia/sp_Syntrophomonas_zehnderi UP000000378_432_phylum_low_GC_Gram+/class_Clostridia/sp_Syntrophothermus_lipocalidus 88 UP000000291_1297_phylum_low_GC_Gram+/class_Clostridia/sp_strain_NAL UP000000467_1604_phylum_low_GC_Gram+/class_Clostridia/sp_Thermoacetogenium_phaeum 51 UP000006866_1247_phylum_low_GC_Gram+/class_Clostridia/sp_strain_GSL 100 92 UP000007434_319_phylum_low_GC_Gram+/class_Clostridia/sp_strain_SL-HP UP000000719_1538_phylum_low_GC_Gram+/class_Clostridia/sp_Halothermothrix_orenii 97 UP000001683_1351_phylum_low_GC_Gram+/class_Clostridia/sp_strain_JW/NM-WN-LF 27 UP000001991_299_phylum_low_GC_Gram+/class_Firmibacteria/sp_Lactobacillus_reuterii UP000002191_930_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfovibrio_aespoeensis 100 UP000011724_641_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfovibrio_piezophilus 94 UP000002601_3389_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Microspira_aestuarii 16 100 UP000007844_96_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfovibrio_africanus UP000009071_830_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfovibrio_magneticus 93 99 UP000027425_1377_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfonatronum_thiodismutans 57 UP000007347_3525_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfobacula_toluolica 50 UP000000718_96_phylum_Thermodesulfovibrio_group/class_Nitrospiria/sp_- UP000004191_367_phylum_low_GC_Gram+/class_Tissierellia/sp_Helococcus_kunzii 25 UP000007102_365_phylum_Aquificaeota/class_Aquificae/sp_strain_BSA UP000030071_4006 97 100UP000033673_2443_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_galatheae 89UP000016895_2349_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_nigripulchritudo UP000002493_199099 UP000002943_1576_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_caribbenthicus 40UP000032303_2023_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_gaetbulicola 92 88UP000033633_917_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_halotolerans 3574UP000032479_1713_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_leiognathi UP000033732_3908_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 63 UP000002675_1896_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_vulnificus UP000033449_1568_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Salinivibrio_sp_KP-1 97 UP000000537_1454_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_noctiluca 83 68UP000006800_389_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000003627_645 94 UP000006683_288_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_PAT 96 UP000030341_370_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudoalteromonas_sp_OCN003 96 UP000033434_4539_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudoalteromonas_luteoviolacea 9194 93UP000033452_3477_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudoalteromonas_rubra UP000033511_3537 64UP000000260_4047_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 80 UP000008543_1224_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Histophilus_somni 93 UP000001485_3558_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 92 UP000031627_557_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_symbiont_bacterium_UwTKB_of_Urostylis_westwoodii UP000000639_3221_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Psychromonas_ingrahamii 100 UP000010320_1598_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Psychromonas_sp_CNPT3 81 UP000006801_1874_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 100 100 UP000033618_429_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_woodsii 99 UP000001693_3952_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Leptothrix_cholodnii Alignment statistics UP000009383_245_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_uncultured_SUP05_cluster_bacterium 87UP000000683_802_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Alteromonas_naphthalenivorans 100 UP000001870_3460_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_DE 98 UP000006327_3735_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Paraglaciecola_arctica 98 91UP000006334_665_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Glaciecola_lipolytica UP000001981_3667_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 9183 UP000004719_210_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_marine_gamma_proteobacterium_HTCC2080 100 96 UP000035013_590_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Spongiibacter_sp_IMCC21906 UP000006242_1145_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Salinisphaera_shabanensis 99 UP000001231_885_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Kangiella_koreensis 100 UP000034071_1936_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Kangiella_geojedonensis Number of taxa: 500 UP000001062_1327_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinomonas_mediterranea 100 UP000001113_4187_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinomonas_sp_MWYL1 UP000003344_1431_phylum_purple_photosynthetic_bacteria_and_relatives/class_-/sp_- 97 91 UP000031392_25_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Neisseria_elongata100 100UP000002768_2233_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Neisseria_sp_oral_taxon_014 100UP000003612_1905_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 100 UP000005837_1548_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 100 100 UP000008291_2438_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Thiobacillus_denitrificans 92 UP000034410_2906_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Sedimenticola_thiotaurini UP000032414_503_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_TATLOCK 69 Alignment length: 119 UP000006286_4011_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Alcanivorax_sp_UVAD 100 UP000008871_2346_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000002714_1733_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Thiomicrospira_denitrificans 96 97UP000007803_1783_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfurimonas_autotrophica 99UP000006431_1816_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfurimonas_gotlandica 98 UP000008721_363_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfuricurvum_kujiense 97 UP000000939_2592_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_strain_CI 100 UP000001136_1825_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Campylobacter_butzleri UP000000799_1330_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_- 74 99 99UP000007727_1152_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Campylobacter_laridis 99 UP000002407_1562_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Candidatus_Campylobacter_hominis Parsimony info. sites: 96.60% 74 100 UP000005709_2283_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Campylobacter_gracilis UP000002222_152_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfurospirillum_deleyianum 96 UP000008633_1705_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Salsamentum_denitrificans UP000000448_717_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_strain_AmH 38 10059UP000001118_261_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Nitratiruptor_sp_SB155-2 UP000005330_538_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Thiovulum_sp_ES UP000002495_1503_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Heliobacterium_hepaticus 100 UP000007032_360_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_canadensis UP000006633_3740_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Thiobacillus_novellus 86 Missing data: 25% 32UP000032611_3983_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Martelella_endophytica 33UP000001600_2354_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Agrobacterium_sp_13-626 30UP000001976_2554_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sinorhizobium_meliloti UP000002930_2765_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodovulum_sp_PH10 83 65 UP000006011_428_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceanicaulis_sp_HTCC2633 73UP000001054_2673_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sinorhizobium_fredii 82UP000009319_2303_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_mesoamericanum UP000004291_2052_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hoeflea_phototrophica 85 UP000003250_4017_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Mesorhizobium_alhagi 100 8293UP000007471_5021_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000002301_1916_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- 14 UP000001820_2409_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_[Mesorhizobium]_sp_BNC1 83UP000008130_3847_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Polymorphum_gilvum UP000008850_2350_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pelagibacterium_halotolerans 16 UP000031643_2917_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methyloceanus_cenitepidus UP000033495_1808_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hyphomonadaceae_bacterium_c29 95 100 32 UP000033765_690_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hyphomonas_sp_c22 97UP000001959_696_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- 95 UP000002745_1211_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hirschia_baltica 75 97 UP000001302_1383_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Parvuliarcular_bermudensis Phylogenetic inference UP000003904_242_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ahrensia_sp_R2A130 76 UP000001023_821_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Silicibacter_pomeroyi 99 34 UP000002703_3804_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodosphaera_minor 34UP000004701_479_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_R2A62 UP000005093_2058_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Silicibacter_lacuscaerulensis 34 UP000008326_3698_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Jannaschina_sp_CCS1 35 UP000019593_1661_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseibacterium_elongatum 10027 UP000004507_861_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Tanella_vestfoldensis UP000006765_438_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceaniovalibus_guishaninsula 84 UP000025047_2864_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Loktanella_hongkongensis UP000001176_517_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Gluconacetobacter_diazotrophicus 67 92 Maximium likelihood 100UP000019231_1567_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sorbose_bacterium 95 UP000006468_2552_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Komagataeibacter_kombuchae 75 100UP000004319_731_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000000948_1619_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ulvina_pasteuriana 77 UP000006746_1132_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Thalassobaculum_marina 79 57 UP000028946_1451_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Candidatus_Caedibacter_acanthamoebae 89 UP000005667_2450_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Azospirillum_lipoferum UP000001591_1419_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodospirillum_centenumRhodocista_centenaria UP000006480_2181_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingobium_sp_AP49 62 87 89 UP000033200_902_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_taxi 84 1000 UFBoot replicates UP000033201_2777_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- 99 UP000033997_3521_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_Ag1 33 UP000001989_2532 94 51 9953UP000018851_339_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sanxanigenens UP000033202_1306_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_changbaiensis 92 UP000032025_2440 UP000012040_1894_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_strain_JSS 100 70 UP000019233_1486_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Bdellovibrio_bacteriovorus 97 31 UP000028183_1343_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_endosymbiont_of_Acanthamoeba_sp_UWC8 UP000018309_917_phylum_purple_photosynthetic_bacteria_and_relatives/class_-/sp_Proteobacteria_bacterium_MGS UP000033468_3258_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodospirillaceae_bacterium_c57 LG+R8 88 UP000007127_1730_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000001935_1654_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Anaeromyxobacter_dehalogenans 100 UP000006382_2183_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Anaeromyxobacter_sp_Fw109-5 UP000017975_1582_phylum_low_GC_Gram+/class_Clostridia/sp_Eubacterium_sp_MGS 61 96UP000018037_705_phylum_low_GC_Gram+/class_Clostridia/sp_Ruminococcus_bromii 55 UP000017996_933_phylum_low_GC_Gram+/class_Clostridia/sp_Eubacterium_sp_MGS 62 UP000004073_1993_phylum_low_GC_Gram+/class_Clostridia/sp_- UP000017926_837_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 100 71 UP000018136_754_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 100 UP000018168_591_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_leptum_MGS 51 UP000018237_1538_phylum_low_GC_Gram+/class_-/sp_Firmicutes_bacterium_MGS 95 UP000018382_239_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS 56 UP000007054_844_phylum_low_GC_Gram+/class_Clostridia/sp_Ruminococcus_champanellensis 89 92UP000017936_1926_phylum_low_GC_Gram+/class_Clostridia/sp_Ruminococcus_sp_MGS 96 100UP000017977_1900_phylum_low_GC_Gram+/class_Clostridia/sp_Ruminococcus_sp_MGS UP000018181_1397_phylum_low_GC_Gram+/class_Clostridia/sp_Ruminococcus_sp_MGS 98 UP000018385_1035_phylum_low_GC_Gram+/class_Clostridia/sp_Anaerotruncus_sp_MGS 100 UP000003803_3605_phylum_low_GC_Gram+/class_Clostridia/sp_Anaerotruncus_colihominis UP000018024_38_phylum_low_GC_Gram+/class_Clostridia/sp_Anaerotruncus_sp_MGS 88 100UP000018414_350_phylum_low_GC_Gram+/class_Clostridia/sp_Eubacterium_sp_MGS UP000018364_1468_phylum_low_GC_Gram+/class_Clostridia/sp_Clostridium_sp_MGS UP000000954_1149_phylum_actinobacteria/class_Coriobacteriia/sp_Cryptobacterium_curtum 57 UP000018042_1682_phylum_actinobacteria/class_Coriobacteriia/sp_Eggerthella_sp_MGS 100 UP000004399_783_phylum_actinobacteria/class_Coriobacteriia/sp_- 80 50 UP000006069_233_phylum_actinobacteria/class_Coriobacteriia/sp_Slackia_piriformis UP000017952_1085_phylum_actinobacteria/class_Coriobacteriia/sp_Collinsella_sp_MGS 98 UP000004830_1948_phylum_actinobacteria/class_Coriobacteriia/sp_Collinsella_tanakaei 38 62UP000018358_1541_phylum_actinobacteria/class_Coriobacteriia/sp_- 9875UP000018185_1225_phylum_actinobacteria/class_Coriobacteriia/sp_strain_phI Taxonomy UP000006851_705_phylum_actinobacteria/class_Coriobacteriia/sp_Coriobacterium_glomerans 96 UP000012651_1252_phylum_actinobacteria/class_Coriobacteriia/sp_- UP000000333_631_phylum_actinobacteria/class_Coriobacteriia/sp_Olsenella_uli 100 10099 UP000003446_608_phylum_actinobacteria/class_Coriobacteriia/sp_- UP000004431_167_phylum_actinobacteria/class_Coriobacteriia/sp_Atopobium_vaginae 96 UP000004070_494_phylum_actinobacteria/class_Coriobacteriia/sp_Lactobacillus_rimae UP000000771_1748_phylum_actinobacteria/class_Acidimicrobiia/sp_strain_ICP 95 88 UP000011863_711_phylum_actinobacteria/class_Acidimicrobiia/sp_Ilumatobacter_coccineus Bacteria UP000006637_1007_phylum_actinobacteria/class_Rubrobacteridae/sp_Rubrobacter_xylanophilus UP000008631_3197_phylum_Planctomycetes/class_Planctomycetia/sp_Torulopsidosira_pallida UP000002524_601_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Micrococcus_radiodurans 49 93 56 UP000007718_1306_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_strain_MRP 93UP000002208_2165_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_deserti 60UP000034024_2470_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_soli 96UP000007575_2803_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_gobiensis Cytophaga-Flexibacter-Bacteroides 99 UP000030634_1225_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_swuensis 99 UP000002431_1865_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_geothermalis UP000008635_1068_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_maricopensis 99 47 UP000010467_488_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_peraridilitoris UP000000379_1257_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Truepera_radiovictrix 100 UP000000532_1928_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_- 96 45UP000008722_1332_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Oceanothermus_profundus Planctomycetes 73 UP000007030_338_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Marinothermus_hydrothermalis UP000000323_756_phylum_-/class_-/sp_Thermobaculum_terrenum 100 99 UP000002349_1542_phylum_green_nonsulfur_bacteria/class_Dehalococcoidia/sp_Dehalogenimonas_lykanthroporepellens 97 UP000002008_2085_phylum_green_nonsulfur_bacteria/class_Chloroflexus/Deinococcus_group/sp_- UP000004508_5173_phylum_green_nonsulfur_bacteria/class_Ktedonobacteria/sp_Ktedonobacter_racemifer UP000000845_2873_phylum_fusobacteria/class_Fusobacteriia/sp_Sphaerophorus_siccus_var_termitidis 99 Aquiﬁcaeota 70 UP000004226_963_phylum_fusobacteria/class_Fusobacteriia/sp_Leptotrichia_goodfellowii UP000033103_338_phylum_fusobacteria/class_Fusobacteriia/sp_Sneathia_amnii 99 UP000001910_1307_phylum_fusobacteria/class_Fusobacteriia/sp_Leptotrichia_buccalis 67 94 59 UP000002072_941_phylum_fusobacteria/class_Fusobacteriia/sp_Streptothrix_muris_ratti 85UP000003415_2318_phylum_fusobacteria/class_Fusobacteriia/sp_Spherophorus_ridiculosu UP000004505_280 93 UP000002521_1606_phylum_fusobacteria/class_Fusobacteriia/sp_Fusobacterium_plauti-vincenti [Plastid donors] 96 Cyanobacteria UP000005392_86 95 99 UP000002975_1439_phylum_fusobacteria/class_Fusobacteriia/sp_- 100 UP000003092_967_phylum_fusobacteria/class_Fusobacteriia/sp_Streptothrix_necuphtora 92 UP000006875_574_phylum_fusobacteria/class_Fusobacteriia/sp_Ilyobacter_polytropus 90 UP000009011_605_phylum_Ignavibacteriae/class_Ignavibacteria/sp_Melioribacter_roseus UP000004671_2420_phylum_Deferribacteres/class_Flexistipes_group/sp_Caldothrix_abyssi [Mitochondrial donors] UP000001110_622_phylum_Thermotogaeota/class_Togobacteria/sp_Thermosipho_melanesiensis Alphaproteobacteria 55 100 100 UP000002415_817_phylum_Thermotogaeota/class_Togobacteria/sp_Fervidobacterium_nodosum UP000008183_28_phylum_Thermotogaeota/class_Togobacteria/sp_- 100 UP000002016_461_phylum_Thermotogaeota/class_Togobacteria/sp_- 100 99 UP000006804_1715_phylum_Thermotogaeota/class_Togobacteria/sp_Thermotoga_thermarum UP000002881_702_phylum_Thermotogaeota/class_Togobacteria/sp_Mesotoga_prima 22 91 99 UP000035159_1582_phylum_Thermotogaeota/class_Togobacteria/sp_Kosmotoga_pacifica Betaproteobacteria UP000002382_1148_phylum_Thermotogaeota/class_Togobacteria/sp_- 99 UP000007161_979_phylum_Thermotogaeota/class_Togobacteria/sp_Marinitoga_piezophila UP000014824_707_phylum_Chlamydiae/class_Chlamydiia/sp_Rickettsiaformis_psittacosis 99 100 88 UP000039860_742_phylum_Chlamydiae/class_Chlamydiia/sp_Rubidus_massiliensis 53 UP000032809_1269_phylum_Thermotogaeota/class_Togobacteria/sp_Defluviitoga_tunisiensis UP000000798_1360_phylum_Aquificaeota/class_Aquificae/sp_Aquifex_aeolicus 99 68 UP000001369_1466_phylum_Aquificaeota/class_Aquificae/sp_Sulfurihydrogenibium_azorense Gammaproteobacteria 43 UP000001732_1108_phylum_low_GC_Gram+/class_Clostridia/sp_Thermobacteroides_proteolyticus UP000019023_933_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfurella_acetivorans UP000001203_4104 47 88 UP000001405_252 55UP000031625_1676 98 UP000001425_70 UP000001688_590 99 Others 78 UP000010389_3981 UP000034681_3059 94 UP000003959_5893 90 UP000010481_2684 64 96 UP000010471_876 87 UP000010473_1325 UP000002384_4457 99 UP000008204_892 UP000002483_849 3590 36UP000010378_2751 Archaea 36UP000010384_2644 36 UP000004344_2810 96 33UP000010101_949 UP000010390_1982 94 UP000019325_2023 88 UP000010472_3826 30 UP000010476_893 Euryarchaeotas UP000010367_5257 9094 UP000010383_528 UP000001332_653 91 UP000010385_1405 5180 UP000000440_2151 UP000006803_3321 51 52 52 UP000010386_679 100 UP000000737_883 UP000010478_704 94 UP000004532_2054 Eukaryota 96 UP000001029_1465_phylum_Elusimicrobia/class_Elusimicrobia/sp_Elusimicrobium_minutum 96 UP000035337_262_phylum_Elusimicrobia/class_Endomicrobia/sp_Endomicrobium_proavitum UP000030902_588_phylum_Saccharobacteria/class_-/sp_Candidatus_Saccharibacteria_oral_taxon_TM7x 99 UP000035655_29_phylum_Saccharobacteria/class_-/sp_Candidatus_Saccharibacteria_bacterium_GW2011_GWC2_44_17 UP000001566_2274 94 91UP000004972_1906_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RS9916 UP000001423_1006 Taxa with plastid/plastid-related organelles 96 UP000001422_254 100 UP000005593_107 88 UP000001420_1530_phylum_cyanophytes/class_-/sp_- 96 88 UP000002535_564 89 98 UP000000788_1435_phylum_cyanophytes/class_-/sp_Prochlorococcus_maritima UP000001026_1734 22 UP000001115_2269_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RCC307 Other eukaryotes 100UP000002935_267_phylum_cyanophytes/class_-/sp_Synechococcus_sp_SYN UP000003950_2739_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7001 96 99 UP000010388_2818_phylum_cyanophytes/class_-/sp_Cyanobium_gracile 64 UP000010366_4516_phylum_cyanophytes/class_-/sp_Sphaerogonium_minutum 77 UP000034681_2861_phylum_cyanophytes/class_-/sp_Prochlorothrix_hollandica UP000008878_4104_phylum_cyanophytes/class_-/sp_Trichodesmium_erythraeum 8085 UP000010367_5628_phylum_cyanophytes/class_-/sp_Phormidium_acuminatum 67 UP000002717_1820 62 UP000010385_1596_phylum_cyanophytes/class_-/sp_Synechococcus_sp_Rippka_B2 UP000005766_1076_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7335 99 53 UP000010472_3270_phylum_cyanophytes/class_-/sp_Crinalium_epipsammum UP000010383_937_phylum_cyanophytes/class_-/sp_Geitlerinema_sp_PCC_7407 76 UP000010386_328_phylum_cyanophytes/class_-/sp_Pseudanabaena_sp_PCC7367 UP000000737_882_phylum_cyanophytes/class_-/sp_Lyngbya_sp_PCC_8106 59 100 97 UP000027395_2975_phylum_cyanophytes/class_-/sp_- 39 UP000006803_3320_phylum_cyanophytes/class_-/sp_- Aano_C6KIQ9 81 UP000000557_2776_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_violaceus 100 41 UP000017396_1283_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_kilaueensis UP000001938_1736_phylum_cyanophytes/class_-/sp_Cyanobacteria_sp_Yellowstone_B-Prime UP000002483_848 93 50 UP000010477_101_phylum_cyanophytes/class_-/sp_Calothrix_parietina 45UP000010378_2231_phylum_cyanophytes/class_-/sp_- 42UP000019325_2022_phylum_cyanophytes/class_-/sp_Nodularia_spumigena 27 22UP000010384_2188_phylum_cyanophytes/class_-/sp_Croococcidiopsis_thermalis 50UP000010381_3706_phylum_cyanophytes/class_-/sp_Nostoc_sp_PCC_7107 UP000001191_5830_phylum_cyanophytes/class_-/sp_Nostoc_punctiforme UP000001511_2538_phylum_cyanophytes/class_-/sp_Trichormus_azollae 3799 100UP000010474_2644_phylum_cyanophytes/class_-/sp_Anabaena_cylindrica UP000010101_2651_phylum_cyanophytes/class_-/sp_- 4294 UP000010390_1632_phylum_cyanophytes/class_-/sp_Calothrix_sp_PCC7507 56 94UP000010475_4492_phylum_cyanophytes/class_-/sp_Cylindrospermum_stagnale UP000004344_2811_phylum_cyanophytes/class_-/sp_- 95 UP000010380_810_phylum_cyanophytes/class_-/sp_Rivularia_sp_LIP 99 UP000010476_361_phylum_cyanophytes/class_-/sp_Chroococcus_sp_Cey_un 74 UP000004532_2055_phylum_cyanophytes/class_-/sp_- 100 53 UP000010478_1139_phylum_cyanophytes/class_-/sp_Oscillatoria_nigroviridis 45UP000003835_3319_phylum_cyanophytes/class_-/sp_Microcoleus_chthonoplastes UP000003959_5894_phylum_cyanophytes/class_-/sp_Moorea_producta UP000000268_5950_phylum_cyanophytes/class_-/sp_- 60 UP000010379_1690_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_6312 62 91 UP000000440_2150_phylum_cyanophytes/class_-/sp_- 92 60 UP000002511_3779_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7425 56 Cpar_riboL1 7335UP000010471_1487_phylum_cyanophytes/class_-/sp_Oscillatoria_sp_Mc UP000001332_197_phylum_cyanophytes/class_-/sp_Oscillatoriales_cyanobacterium_JSC-12 UP000002384_4152_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7424 99 67UP000008206_147_phylum_cyanophytes/class_-/sp_Cyanothece_sp_PCC_7822 UP000010382_532_phylum_cyanophytes/class_-/sp_Pleurocapsa_minor UP000001203_4103 7274 89 UP000031625_588_phylum_cyanophytes/class_-/sp_cyanobacterium_endosymbiont_of_Epithemia_turgida 72 UP000008204_891_phylum_cyanophytes/class_-/sp_- UP000001405_251_phylum_cyanophytes/class_-/sp_cyanobacterium_UCYN-A 93 UP000001510_2715_phylum_cyanophytes/class_-/sp_Microcystis_aeruginosa UP000001688_589_phylum_cyanophytes/class_-/sp_- 74 100 UP000010389_3799_phylum_cyanophytes/class_-/sp_Leptolyngbya_sp_PCC_7376 UP000001425_69_phylum_cyanophytes/class_-/sp_- 98 UP000010473_2169_phylum_cyanophytes/class_-/sp_Stanieria_cyanosphaera 74 UP000010481_3247_phylum_cyanophytes/class_-/sp_Aphanothece_halophytica_'Solar_Lake' 92 UP000010480_84_phylum_cyanophytes/class_-/sp_Cyanobacterium_aponinum 100 UP000010483_1842_phylum_cyanophytes/class_-/sp_Cyanobacterium_stanieri Atha_13227 100 Atha_15720 100 Bdis_2g26940 100 99 Sbic_09g019170 96 99Acoe_009_00347 Mgut_mgv1a009175m 100 24 Mgut_mgv1a011815m Smoe_XP_002965341 25 100 Smoe_XP_002977183 96 Kfla_7851 Ppat_XP_001753672 99 99Ppat_XP_001771425 87 Mpol_1864 Crei_XP_001701761 100 99 100 Vcar_XP_002946388 99 Cvar_EFN51465 Mpus_Micpu126974 Tpse_XP_002297540 100 100 Toce_26154 74 Ptri_YP_874396 Esil_CAT18712 61 Vbra_9993 96 81 72 Gsul_2653 Cmer_CMV103C 89 Ngad_6507 Ehux_468608 100 88 Ehux_59686 Bnat_92333

0.8 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which Supplementarywas not certified by peer ﬁ review)gure is the 6author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. UP000009004_2062_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 93 100 UP000000233_1901 100 UP000019522_3658_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_stutzeri UP000005437_1656 100 UP000002332_5900_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 100 UP000027583_2708_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Asaia_platycodi 85 85 UP000000223_3516_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Salmonella_gluconica 100 UP000001695_1461_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Beijerinckia_indica 100 UP000000948_2555_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ulvina_pasteuriana 100 UP000004319_2072_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000027249_1385_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_cf_campisalis_'campaniae' 100 UP000018258_2044_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_sp_A3H3 100 UP000033642_1039_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_sp_S2151 100 UP000008707_828_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_elongata UP000033673_3033_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_galatheae 56 100 100 UP000030071_936 95 UP000029660_842_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_coralyticus UP000007456_1314_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_furnissii 61 100 UP000002493_801 46 100 UP000002675_871_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_vulnificus 58 UP000009073_2926_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Tolumonas_auensis UP000007077_1732_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 100 61 UP000000998_171 UP000005953_744_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Reinekia_blandensis 100 UP000032266_1985_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Gynuella_sunshinyii 91 UP000002171_2503_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Neptuniibacter_caesariensis UP000001113_2756_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinomonas_sp_MWYL1 100 UP000001062_1583_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinomonas_mediterranea 57 UP000011864_3849_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Paraglaciecola_psychrophila 100 100 UP000006327_3635_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Paraglaciecola_arctica 100 UP000006334_1284_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Glaciecola_lipolytica UP000000547_107_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_psychroerythus 57 UP000005555_2115_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_marine_gamma_proteobacterium_HTCC2207 100 100 UP000004931_2152_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_marine_gamma_proteobacterium_HTCC2143 UP000033581_1768_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Gammaproteobacteria_bacterium_c0 UP000009100_4290_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_tasmaniensis 34 100 UP000003769_3130_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_shilonii 99 UP000032303_4795_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_gaetbulicola 99 100 UP000033732_1623_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000001982_63_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_denitrificans 99 99 UP000000593_2717_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_profundum 80 UP000000466_1407_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Simiduia_agarivorans 100 100 UP000001036_2191_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_fluorescens_subsp_cellulosa 100 UP000011866_1395_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Thalassolituus_oleivorans UP000009080_1992_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Teredinibacter_turnerae 100 UP000001947_1647_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Saccharophagus_degradans 69 UP000001993_1489_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Psychrobacter_sp_PRwf-1 UP000008315_851_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylomicrobium_alcaliphilum 100 UP000008888_4138_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_methanica 100 UP000005090_2720_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylomonas_albus 100 78 UP000004664_708_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylobacter_tundripaludum UP000004692_118_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_gamma_proteobacterium_HTCC5015 73 80 UP000002713_1031_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Thiomicrospira_crunogena 100 94 UP000005380_1235_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Thioalkalimicrobium_aerophilum UP000004263_1026_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Bermanella_marisrubri UP000035013_2598_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Spongiibacter_sp_IMCC21906 100 86 UP000003473_827_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Zhongshania_aliphaticivorans 69 UP000006282_187_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000008871_1646_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 100 UP000006286_2629_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Alcanivorax_sp_UVAD UP000002716_1032_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shigella_shigae 100 100UP000003488_558_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shigella_paradysenteriae 74 UP000000625_259 UP000003488_8542 99 84 UP000032876_2277_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Citrobacter_werkmanii 94 UP000008148_4612 79 UP000001889_2034 99UP000001014_2431_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000002084_2773_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Salmonella_enterica_ser_choleraesuis UP000029498_300 99 85 96 UP000037393_985_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Trabulsiella_odontotermitis 97 UP000000265_3606_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 75 UP000011002_418_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Enterobacteriaceae_bacterium_strain_FGI_57 UP000017834_3163 100 27 UP000006497_5717 75 100 UP000000230_3739 100 UP000035479_5369 100 UP000009361_4113_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Cronobacter_dublinensis 100 UP000000260_2275 UP000029516_1363_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Cedecea_neteri UP000019587_50_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Yersinia_enterocolitica 68 100 94 UP000000815_1342_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Yersinia_pseudotuberculosis_subsp_pestis 100 UP000007074_4541 100 UP000011001_4232 53 UP000029986_3979_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Hafnia_alvei 83 UP000009010_616 UP000001624_3329 100 92 UP000006631_3094 UP000030310_2671 80 99 69 UP000008793_4670_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Erwinia_billingiae UP000007966_466 UP000008319_1825_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Proteus_mirabilis 100 100 99 UP000011834_2764_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Salmonella_morgani UP000008075_1029_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Xenorhabdus_nematophilus_subsp_nematophilus 86 UP000030901_489_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Frischia_perrara 100 UP000019656_45_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Gilliamella_apicola UP000002350_562_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_violacea 100 100 UP000003579_3056_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_damselae UP000009073_990 100 UP000000756_3925_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000002287_4856_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 97 97 UP000003049_6408_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_sp_TJI49 100 UP000001035_5212_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_cepacia_genomovar_IIIb UP000032634_321_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_uboniae 100 UP000008316_6031_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_gladioli 100 47 55 96 UP000002187_3456_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_glumae UP000000605_1147_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_pseudomallei 80 UP000033618_296_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_woodsii UP000006801_2572_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- UP000032614_2585_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Paraburkholderia_fungorum 70 83 82 UP000037921_1201 100 UP000001817_6371_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Paraburkholderia_xenovorans UP000002190_1277_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_sp_CCGE1002 83 100 UP000001550_719_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_sp_CCGE1003 100 94 UP000001550_1625 79 UP000037921_2448_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_sp_ST111 UP000001192_6136_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Paraburkholderia_phymatum UP000004277_590_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_sp_PBA UP000007507_80_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbaspirillum_sp_YR522 100 82 100 UP000000329_3456_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbispirillum_seropedicense 100 UP000007296_3134_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbaspirillum_sp_CF444 90 UP000008392_2964_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Collimonas_group_C Alignment statistics UP000027604_3342_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Janthinobacterium_agaricidamnosum 100 UP000034315_2788_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 41 UP000031843_7349 57 100 100 UP000002429_1509_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- Number of taxa: 271 49 UP000008210_1847_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Wautersia_eutropha UP000001436_488_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_solanacearum 100 UP000002566_4011_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_pickettii 81 UP000001693_3753_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Leptothrix_cholodnii 100 UP000035352_820_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_[Polyangium]_brachysporum Alignment length: 786 UP000000784_2374_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_indoloxidans 98 100 100 99 UP000004811_1366_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Acidovorax_sp_CF316 100 UP000002440_2399_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_strain_KT 83 UP000002588_1166_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- Parsimony info. sites: 85.20% UP000024387_549_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Dyella_jiangningensis UP000003704_3599_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Hydrocarbophaga_effusa 100 UP000018418_2268_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Acinetobacter_brisouii 90 91 UP000017667_701_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000000430_1578 Missing data: 0.64% 100 UP000032870_367_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Acinetobacter_sp_HR7 99 98 UP000018419_676 UP000013121_843_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Acinetobacter_guillouiae UP000001889_1661_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Citrobacter_rodentium 100 100 UP000008148_1238 98 UP000000230_2287_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 99 UP000035479_5283_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Kluyvera_intermedia 100 UP000000265_2143 Phylogenetic inference UP000000260_3221_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000001702_352_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Xanthomonas_uredovorus 100 100 100 UP000006631_1102 99 100 UP000029498_4428_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pluralibacter_gergoviae 98 UP000030310_3143_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pantoea_sp_PSNIH2 Maximium likelihood UP000019028_3055_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_HS UP000001726_3264_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Erwinia_tasmaniensis 100 100 100 UP000009010_3480_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Rahnella_aquatilis 100 UP000017834_684_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Enterobacter_hormaechei_subsp_grimontii 1000 UFBoot replicates UP000011001_1976_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 100 UP000007074_2872_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Xantomonas_proteamaculans UP000002759_223_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Brenneria_sp_EniD312 44 93 100 96 UP000044377_4085_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Brenneria_goodwinii LG+F+R10 100 UP000007966_1534_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pectobacterium_carotovorum_var_atrosepticum 100 UP000006497_5420_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Kosakonia_radicincitans UP000006859_3403_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000006764_1974_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Alcanivorax_pacificus 100 UP000019805_2837_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Castellaniella_defragrans UP000010389_819_phylum_cyanophytes/class_-/sp_Leptolyngbya_sp_PCC_7376 58 73 UP000000268_7719_phylum_cyanophytes/class_-/sp_- UP000010366_5249_phylum_cyanophytes/class_-/sp_Sphaerogonium_minutum 99 UP000010478_1704_phylum_cyanophytes/class_-/sp_Oscillatoria_nigroviridis 100 100 100 UP000004532_1922_phylum_cyanophytes/class_-/sp_- UP000010471_4037_phylum_cyanophytes/class_-/sp_Oscillatoria_sp_Mc UP000002139_4225_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Sorangium_nigrum UP000013968_2687_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_orientalis 100 100 UP000003970_4072_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_sp_AA4 100 100 UP000006138_7782_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_mediterranei 100 UP000004926_4868_phylum_actinobacteria/class_high_GC_Gram+/sp_Saccharomonospora_marina UP000019225_825_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptosporangium_albidum UP000003653_3241_phylum_actinobacteria/class_high_GC_Gram+/sp_Mycobacterium_parascrofulaceum 98 100 100 UP000001190_3584_phylum_actinobacteria/class_high_GC_Gram+/sp_Mycobacterium_platypoecilus 100 UP000018763_1009_phylum_actinobacteria/class_high_GC_Gram+/sp_- 96 99 UP000005845_1166_phylum_actinobacteria/class_high_GC_Gram+/sp_Rhodococcus_sputi UP000006728_3534_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptomyces_erythraeus UP000037694_4761_phylum_actinobacteria/class_high_GC_Gram+/sp_Nocardiopsis_sp_NRRL_B-16309 100 99 UP000002219_172 UP000003448_5759_phylum_actinobacteria/class_high_GC_Gram+/sp_Micromonospora_lupini 100 100 UP000037709_4013_phylum_actinobacteria/class_high_GC_Gram+/sp_Micromonospora_sp_NRRL_B-16802 93 UP000008308_3874_phylum_actinobacteria/class_high_GC_Gram+/sp_Verrucosispora_maris 80 UP000002484_716_phylum_actinobacteria/class_high_GC_Gram+/sp_Frankia_sp_EuI1c 98 UP000009236_573_phylum_actinobacteria/class_high_GC_Gram+/sp_Isoptericola_variabilis 100 UP000002255_613_phylum_actinobacteria/class_high_GC_Gram+/sp_Xylanomonas_cellulosilytica 83 82 100 UP000034098_2943_phylum_actinobacteria/class_high_GC_Gram+/sp_Microbacterium_trichothecenolyticum UP000008366_3511_phylum_actinobacteria/class_high_GC_Gram+/sp_Kineosphaera_limosa 99 UP000002029_1283_phylum_actinobacteria/class_high_GC_Gram+/sp_Streptosporangium_roseum 100 UP000001918_857_phylum_actinobacteria/class_high_GC_Gram+/sp_Thermomonospora_curvata UP000001937_3639_phylum_actinobacteria/class_high_GC_Gram+/sp_Frankia_sp_CcI3 100 100 99 UP000000657_5294_phylum_actinobacteria/class_high_GC_Gram+/sp_no_culture_available UP000030300_4738_phylum_actinobacteria/class_high_GC_Gram+/sp_Pimelobacter_simplex 100 100 100 UP000033772_4855_phylum_actinobacteria/class_high_GC_Gram+/sp_Nocardioides_luteus UP000015971_992_phylum_actinobacteria/class_high_GC_Gram+/sp_Nocardioides_sp_CF8 UP000007575_3095_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_gobiensis 100 UP000002431_2954_phylum_Thermus/Deinococcus_group/class_Hadobacteria/sp_Deinococcus_geothermalis UP000004947_1252_phylum_Lentisphaeraeota/class_Lentisphaeria/sp_Lentisphaera_araneosa 100 UP000000925_552_phylum_verrucomicrobia/class_Opitutae/sp_Coraliomargarita_akajimensis UP000002534_491_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Pelobacter_carbinolicus UP000003586_1377_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Niabella_soli 66 96 UP000002215_2315_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Chitinophaga_pinensis 100 UP000005438_2929_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Niastella_koreensis UP000003664_166_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Sphingobacteriia/sp_Pedobacter_sp_BAL39 99 100 UP000033121_3697_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Flavihumibacter_petaseus UP000007590_3549_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Sphingobacteriia/sp_[Flexibacter]_canadensis 100 UP000002774_3007_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Sphingobacteriia/sp_Mucilaginibacter_paludis 100 UP000011058_4293_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Fibrella_aestuarina 100 100 100 UP000002028_1316_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Spirosoma_linguale 95 100 UP000002011_2045_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Dyadobacter_fermentens UP000009309_2495_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Fibrisoma_limi UP000001822_2278_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Cytophaga_hutchinsonii 100 97 UP000000493_1397_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Runella_slithyformis Taxonomy UP000010796_2200_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Echinicola_vietnamensis 100 100 UP000001635_3015_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_strain_Raj 97 UP000006073_2636_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Indibacter_alkaliphilus Bacteria UP000007808_1183_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Sphingobacteriia/sp_Sphingobacterium_sp_21 UP000008634_1774_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Cellulophaga_algicola 100 100 UP000007487_867_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Cytophaga_lytica Cytophaga-Flexibacter-Bacteroides (Phylum) 100 99 UP000008898_3987_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_strain_Dsij UP000008908_121_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Muricauda_ruestringensis 100 100 Planctomycetes(Phylum) 100 UP000016160_731_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Formosa_agariphila UP000032229_1994_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Siansivirga_zeaxanthinifaciens UP000004690_2922_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Joostella_marina Aquiﬁcaeota (Phylum) 100 100 UP000007364_383_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Galbibacter_marinus 100 100 97 UP000003919_1103_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Algoriphagus_machipongonensis Cyanophytes (Phylum) [Plastid donors] 100 UP000006694_434_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Flexibacter_aurantiacus 100 UP000007287_2572_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Flavobacterium_sp_CF136 UP000008461_6196_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Haliscomenobacter_hydrossis Purple photosynthetic bacteria and relatives (Phylum) UP000004889_2868_phylum_Spirochaetes/class_Spirochaetia/sp_Leptospira_licerasiae 100 100 UP000001847_1509_phylum_Spirochaetes/class_Spirochaetia/sp_strain_Patoc_I UP000005737_3733_phylum_Spirochaetes/class_Spirochaetia/sp_Leptospira_illini Alpha subgroup [Mitochondrial donors] UP000003087_3029_phylum_Planctomycetes/class_Planctomycetia/sp_Planctomyces_maris 100 UP000004358_4856_phylum_Planctomycetes/class_Planctomycetia/sp_Pivellula_marina Aory_CADAORAT00006175 Beta subgroup 100 100 Anid_7892 99 Tmel_XP_002841192 Gamma subgroup 100 Ncra_4204NCU04720 100 Fgra_CEF76735 Bade_5354 Delta subgroup 100 100 Opar_3131 Ccin_CC1G_07228 100 94 Umay_XP_759995 Others Uram_177615 100 97 Mcir_Mucci2_73657 Rirr_3245 100 Archaea 78 Rirr_250550 Clim_g4940 82 79 Spun_SPPG_07925 Euryarchaeotas (Phylum) 100 Gpro_158697 Pult_9450 100 Pinf_XP_002900554 100 100 Sarc_SARC_08918 100 Eukaryota Cfra_4044T1 Aker_101422 93 Taxa with plastid/plastid-related organelles 100 Sagg_75322 99 Alim_86378 Tpse_XP_002287665 100 Other eukaroytes 100 Toce_16230 100 Ptri_XP_002180792 100 100 Aano_F0Y6U7 Esil_CBJ31380 Smin_040143_t1 100 100 Smin_036678_t1 100 Vbra_16973 Vbra_1590

0.2 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which Supplementarywas not certified by peer ﬁreview)gure is the author/funder,7 who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license.

UP000001036_2197_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_fluorescens_subsp_cellulosa 100 UP000003395_3984_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Cellvibrio_sp_BR 83 UP000032266_3355_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Gynuella_sunshinyii 92 82 UP000033581_1322_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Gammaproteobacteria_bacterium_c0 UP000001947_1724_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Saccharophagus_degradans 95 88 UP000009080_1965_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Teredinibacter_turnerae UP000000238_1221_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Hahella_chejuensis 87 18 UP000003839_387_phylum_verrucomicrobia/class_Verrucomicrobiae/sp_Verrucomicrobiales_bacterium_DG1235 UP000001947_1723 Alignment statistics 90 68 UP000002677_2510_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_gamma_proteobacterium_HdN1 UP000000925_1714_phylum_verrucomicrobia/class_Opitutae/sp_Coraliomargarita_akajimensis 77 UP000003473_826_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Zhongshania_aliphaticivorans 100 57 UP000035013_2254_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Spongiibacter_sp_IMCC21906 UP000004692_115_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_gamma_proteobacterium_HTCC5015 53 UP000006764_469_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Alcanivorax_pacificus 94 100 Number of taxa: 393 UP000008871_1647_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 85 UP000004263_1029_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Bermanella_marisrubri UP000004374_900_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Rheinheimera_nanhaiensis 100 99 UP000034895_2827_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Arsukibacterium_sp_MJ3 91 52 UP000002168_1651_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_woodyi 100 UP000000466_1991_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Simiduia_agarivorans UP000000238_2963 Alignment length: 441 UP000005167_46_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000002587_623_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Ruthia_magnifica 90 100 100 UP000009383_22_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_uncultured_SUP05_cluster_bacterium 100 UP000015562_562_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_endosymbiont_of_unidentified_scaly_snail_isolate_Monju 100 UP000015559_2253_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Sulfuricella_denitrificans 90 UP000006282_656_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- Parsimony info. sites: 97.50% 88 95 UP000035081_2041_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinobacter_salarius UP000003255_1323_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Beggiatoa_sp_PS UP000004664_726_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylobacter_tundripaludum 100 100 UP000005090_2722_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylomonas_albus UP000008888_3155_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_methanica 100 100 UP000008315_850_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylomicrobium_alcaliphilum Missing data: 6.09% 100 UP000008888_4137 UP000003544_2465_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_MP 100 UP000004679_918_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylophaga_thiooxydans 84 100 UP000009144_2525_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylophaga_nitratireducenticrescens 97 95 UP000009145_1031_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylophaga_frappieri UP000003395_3986 UP000001993_1488_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Psychrobacter_sp_PRwf-1 UP000000593_2719_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_profundum 93 100 UP000032303_3026_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_gaetbulicola 99 UP000033732_1276_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000001982_65_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_denitrificans 100 UP000003769_3132_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_shilonii Phylogenetic inference 100 UP000009100_4292_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_tasmaniensis 10099 100 UP000000639_981_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Psychromonas_ingrahamii 92 UP000001870_2642_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_DE UP000000466_627 10086 UP000011866_3183_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Thalassolituus_oleivorans UP000032749_1015_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Oleispira_antarctica 98 Maximium likelihood UP000002171_2501_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Neptuniibacter_caesariensis 100 100 UP000009073_2928_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Tolumonas_auensis 98 UP000000547_104_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_psychroerythus 100 UP000001981_1866_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 99 100 UP000006327_4675_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Paraglaciecola_arctica UP000006334_450_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Glaciecola_lipolytica 100 UP000002168_4080 1000 UFBoot replicates 100 100 UP000002350_4058_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_violacea 100 UP000002608_1769_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_pealeii 100 UP000000684_2492_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_livingstonis UP000032438_3936_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_viscosus UP000001302_2294_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Parvuliarcular_bermudensis UP000001422_138 LG+F+R10 100 100 UP000004972_1742_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RS9916 100UP000001422_137 100UP000001566_2435 100 UP000001115_2399_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RCC307 UP000003950_342_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7001 100 UP000000268_6634_phylum_cyanophytes/class_-/sp_- 87 UP000005766_3480_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7335 100 UP000001688_1267_phylum_cyanophytes/class_-/sp_- 87 UP000010389_749_phylum_cyanophytes/class_-/sp_Leptolyngbya_sp_PCC_7376 98 UP000001203_2286 100 99 UP000003922_3070_phylum_cyanophytes/class_-/sp_Erythrosphaera_marina 96 UP000008204_3294_phylum_cyanophytes/class_-/sp_- 98 82 UP000002384_3395_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7424 88 UP000010473_1571_phylum_cyanophytes/class_-/sp_Stanieria_cyanosphaera 81 UP000010380_450_phylum_cyanophytes/class_-/sp_Rivularia_sp_LIP 98 UP000003959_5971_phylum_cyanophytes/class_-/sp_Moorea_producta UP000006803_5208_phylum_cyanophytes/class_-/sp_- 98 98 100 UP000008878_3431_phylum_cyanophytes/class_-/sp_Trichodesmium_erythraeum UP000000737_1160_phylum_cyanophytes/class_-/sp_Lyngbya_sp_PCC_8106 75 UP000003835_5567_phylum_cyanophytes/class_-/sp_Microcoleus_chthonoplastes UP000010367_5638_phylum_cyanophytes/class_-/sp_Phormidium_acuminatum UP000001191_2320_phylum_cyanophytes/class_-/sp_Nostoc_punctiforme 97 UP000010381_1996_phylum_cyanophytes/class_-/sp_Nostoc_sp_PCC_7107 Taxonomy 63 UP000010475_3052_phylum_cyanophytes/class_-/sp_Cylindrospermum_stagnale 99 UP000010101_2024_phylum_cyanophytes/class_-/sp_- 100 63 UP000010474_1448_phylum_cyanophytes/class_-/sp_Anabaena_cylindrica 21 69 UP000010390_1814_phylum_cyanophytes/class_-/sp_Calothrix_sp_PCC7507 Bacteria UP000010384_3423_phylum_cyanophytes/class_-/sp_Croococcidiopsis_thermalis 72 76 UP000010472_2969_phylum_cyanophytes/class_-/sp_Crinalium_epipsammum 100 UP000004344_492_phylum_cyanophytes/class_-/sp_- 35 100 UP000008206_5193_phylum_cyanophytes/class_-/sp_Cyanothece_sp_PCC_7822 Cytophaga-Flexibacter-Bacteroides (Phylum) 36 UP000010478_827_phylum_cyanophytes/class_-/sp_Oscillatoria_nigroviridis 38 UP000005766_1945 100 38 UP000010380_5873 100 UP000010384_3713 Planctomycetes (Phylum) 36 UP000019325_1418_phylum_cyanophytes/class_-/sp_Nodularia_spumigena UP000010471_292_phylum_cyanophytes/class_-/sp_Oscillatoria_sp_Mc 36 UP000010379_528_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_6312 Aquiﬁcaeota (Phylum) 100 UP000010383_273_phylum_cyanophytes/class_-/sp_Geitlerinema_sp_PCC_7407 UP000010481_1965_phylum_cyanophytes/class_-/sp_Aphanothece_halophytica_'Solar_Lake' UP000018258_4240 100 UP000027249_3392 Cyanophytes (Phylum) [Plastid donors] 100 UP000001962_1860_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Alkalilimnicola_ehrlichii 100 UP000000998_3045 100 100 UP000011757_2794_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinobacter_sp_BSs20148 UP000000233_875 Purple photosynthetic bacteria and relatives (Phylum) 100 100 UP000033602_2488_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_xanthomarina 100 UP000009004_3356_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000000546_1520_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Psychrobacter_arcticus 100 100 100 UP000001993_657 Alpha subgroup [Mitochondrial donors] UP000007029_1793_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_denitrificans UP000033681_459_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Flavobacteriales_bacterium_c54 100 UP000001258_3418_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_halodurans 99 99 UP000001544_2877_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_pseudofirmus Beta subgroup 99 UP000001401_3656_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_cellulosilyticus UP000000271_105_phylum_low_GC_Gram+/class_Firmibacteria/sp_[Bacillus]_selenitireducens UP000001225_3451 100 UP000006876_5812_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Alcaligenes_xylosoxydans_xylosoxydans Gamma subgroup 99 UP000002768_1730_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Neisseria_sp_oral_taxon_014 100 UP000004105_1886_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Neisseria_bacilliformis 100 99 UP000001983_934_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Polaromonas_sp_JS666 100 Delta subgroup UP000003856_1818_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_delafieldii 66 100 UP000000366_1681_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Methylibium_petroleiphilum UP000002186_426_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Thauera_sp_MZ1T 100 100 UP000006552_885_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Aromatoleum_aromaticum UP000034410_219_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Sedimenticola_thiotaurini Others UP000003250_5534_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Mesorhizobium_alhagi 100 100 UP000008850_810_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pelagibacterium_halotolerans 100 99 UP000031643_946_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methyloceanus_cenitepidus 96 UP000007730_535_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pseudomonas_carboxydovorans 100 UP000001868_2705_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Phenylobacterium_zucineum Archaea 100 UP000033997_2076_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_Ag1 UP000008207_6905_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methylobacterium_nodulans 100 97 UP000011859_2271_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000004218_2303_phylum_actinobacteria/class_high_GC_Gram+/sp_Oospora_matruchoti Euryarchaeotas(Phylum) 100 65 UP000033457_1911_phylum_actinobacteria/class_high_GC_Gram+/sp_Corynebacterium_murium UP000000432_783_phylum_low_GC_Gram+/class_Firmibacteria/sp_Streptobacterium_plantarum 100 UP000004625_3041_phylum_low_GC_Gram+/class_Firmibacteria/sp_Lactobacillus_parashochufarrago 100 UP000003070_131_phylum_low_GC_Gram+/class_Firmibacteria/sp_Lactobacillus_oris 100 100 UP000006910_625_phylum_low_GC_Gram+/class_Firmibacteria/sp_Lactobacterium_fermentum Eukaryota 95 UP000034887_1161_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_SA1-12 100 UP000001908_1388_phylum_actinobacteria/class_high_GC_Gram+/sp_- 100 94 UP000005442_3466_phylum_actinobacteria/class_high_GC_Gram+/sp_Mycobacterium_rhodesiense UP000006315_2478_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_azotoformans Taxa with plastid/plastid-related organelles 96 100 UP000006316_2447_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_bataviensis UP000009283_1026_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_coagulans 100 UP000006821_2364_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylococcus_capsulatus UP000000740_481_phylum_euryarchaeotes/class_Halomebacteria/sp_Halorubrum_lacusprofundi Other eukaroytes 100 UP000002698_727_phylum_euryarchaeotes/class_Halomebacteria/sp_strain_Gabara 77 UP000010878_2121_phylum_euryarchaeotes/class_Halomebacteria/sp_Natronococcus_occultus 83 92 UP000019024_1429_phylum_euryarchaeotes/class_Halomebacteria/sp_Halostagnum_larsenii 69 UP000000390_1019_phylum_euryarchaeotes/class_Halomebacteria/sp_Halalkalicoccus_jeotgali 100 UP000001903_731_phylum_euryarchaeotes/class_Halomebacteria/sp_Haloterrigena_turkmenicus UP000006794_2678_phylum_euryarchaeotes/class_Halomebacteria/sp_Halopiger_xhanaduii UP000002215_2312_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Chitinophaga_pinensis 100 100 UP000005438_2926_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Niastella_koreensis 100 UP000002774_3011_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Sphingobacteriia/sp_Mucilaginibacter_paludis 100 UP000007808_1188_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Sphingobacteriia/sp_Sphingobacterium_sp_21 UP000003586_3111_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Niabella_soli 100 UP000000493_2011_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Runella_slithyformis 100 UP000009309_2498_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Fibrisoma_limi 100 100 UP000002028_1312_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Spirosoma_linguale UP000002011_2048_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Dyadobacter_fermentens 100 100 99 UP000011058_4290_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Fibrella_aestuarina UP000007590_3546_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Sphingobacteriia/sp_[Flexibacter]_canadensis 99 100 UP000033121_4135_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Chitinophagia/sp_Flavihumibacter_petaseus 84 UP000001822_2291_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Cytophaga_hutchinsonii UP000034883_1304_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Sandaracinus_amylolyticus 84 UP000001635_3019_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_strain_Raj 100 UP000010796_1928_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Echinicola_vietnamensis 54 100 UP000006073_2635_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Indibacter_alkaliphilus UP000001847_1514_phylum_Spirochaetes/class_Spirochaetia/sp_strain_Patoc_I 100 UP000005737_3737_phylum_Spirochaetes/class_Spirochaetia/sp_Leptospira_illini UP000000671_7458_phylum_Fibrobacteres/Acidobacteria_group/class_Solibacteres/sp_Solibacter_usitatus 89 89 UP000002220_1880_phylum_Planctomycetes/class_Planctomycetia/sp_Planctopirus_limnophilus 82 89 UP000010798_5465_phylum_Planctomycetes/class_Planctomycetia/sp_Singulisphaera_acidiphila 86 UP000003087_3028_phylum_Planctomycetes/class_Planctomycetia/sp_Planctomyces_maris UP000005943_1948_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_MED193 78 100 UP000005964_3143_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_SK209-2-6 UP000002221_1430_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_-/sp_Rhodothermus_obamensis UP000008634_1772_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Cellulophaga_algicola 100 43 100 UP000008898_1745_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_strain_Dsij 100 UP000008908_123_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Muricauda_ruestringensis 100 UP000016160_736_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Formosa_agariphila UP000003919_1098_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Cytophagia/sp_Algoriphagus_machipongonensis 100 98 83 UP000004690_2917_phylum_Cytophaga-Flexibacter-Bacteroides_phylum/class_Flavobacteriia/sp_Joostella_marina UP000004947_3149_phylum_Lentisphaeraeota/class_Lentisphaeria/sp_Lentisphaera_araneosa UP000000239_2168_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 43 44 UP000008707_804_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_elongata UP000033642_2416_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_sp_S2151 100 UP000018258_1469_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_sp_A3H3 100 100 UP000027249_633_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Halomonas_cf_campisalis_'campaniae' UP000006242_2222_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Salinisphaera_shabanensis 59 UP000007127_2333_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- 100 97 97 UP000033468_3229_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodospirillaceae_bacterium_c57 UP000037884_2074_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_AAP38 UP000031623_2421_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Thioploca_ingrica UP000002287_4857_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 100 100UP000032941_2954 100 UP000001035_5213_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_cepacia_genomovar_IIIb 100 UP000003049_6407_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_sp_TJI49 98 UP000032634_2793_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_uboniae UP000000605_1146_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_pseudomallei 100 UP000002187_3455_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_glumae 100 69 100 UP000008316_6032_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_gladioli UP000001225_2241_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Bordetella_petrii UP000001192_6135_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Paraburkholderia_phymatum 86 100 UP000001550_718_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_sp_CCGE1003 100 97 UP000037921_2309_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_sp_ST111 UP000006801_2573_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 83 UP000000329_3455_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbispirillum_seropedicense 100 100 UP000007507_2881_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbaspirillum_sp_YR522 UP000007296_652_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbaspirillum_sp_CF444 65 UP000027604_3265_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Janthinobacterium_agaricidamnosum 100 100 UP000034315_1726_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 92 UP000008392_2963_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Collimonas_group_C UP000002566_4010_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_pickettii 100 100UP000031501_4670_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- 100UP000031501_5708 98 UP000001436_487_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_solanacearum 89 UP000005808_190_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Wautersia_basilensis 100 100 UP000031843_6245 47 UP000008210_1846_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Wautersia_eutropha UP000006286_116_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Alcanivorax_sp_UVAD 49 UP000002139_6043_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Sorangium_nigrum 48 UP000024387_912_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Dyella_jiangningensis UP000003704_2275_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Hydrocarbophaga_effusa UP000006309_81046_phylum_-/class_-/sp_uncultured_eubacterium 100 UP000032870_1316_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Acinetobacter_sp_HR7 100 88 98 UP000013121_859_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Acinetobacter_guillouiae 100 UP000018419_677 99 UP000000430_1577 100 UP000017667_2582_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- 100 UP000017667_2220 UP000018418_2884_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Acinetobacter_brisouii Mgut_mgv1a004568m 100 100Mgut_mgv1a005457m Mgut_mgv1a027122m 100 Mgut_mgv1a022931m 100 38 Mgut_mgv1a023402m Ntab_3789 100 96 Ntab_3446 Mgut_mgv1a025664m 43 Mgut_mgv1a004332m 96 Atha_1756 100 100 Atha_30033 Mgut_mgv1a004788m 100 Atha_11637 100 100 Atha_18762 Atha_16968 100 Bdis_3g01290 100 60 Bdis_3g01277 Sbic_04g000970 64 Bdis_3g01270 99 9 100 Bdis_3g01250 61 Sbic_04g001000 Acoe_030_00093 100 Acoe_030_00092 Smoe_XP_002966266 99 Smoe_XP_002993278 Bdis_2g40740 100 80 100 Sbic_03g025300 Atha_25512 100 Mgut_mgv1a005911m 100 Mgut_mgv1a005636m 100 100 Mgut_mgv1a006145m Acoe_002_00060 Mgut_mgv1a019058m 100 100 100 Mgut_mgv1a004977m 99 Mgut_mgv1a023971m 97 Atha_3537 Bdis_2g47640 99 100 100 Sbic_03g032310 Acoe_002_00061 Mpol_8180 100 100Mpol_14273 100Mpol_15963 100Mpol_16082 100 Mpol_14780 100 Mpol_9278 Mpol_13200 100 100 Mpol_10920 100 Mpol_11433 100 Mpol_6345 100 100 Mpol_17009 100 Mpol_10947 Mpol_13516 Ppat_XP_001785194 100 Ppat_XP_001768210 99 100 93 Ppat_XP_001768212 Ppat_XP_001765331 100 Ppat_XP_001768801 100 Ppat_XP_001754049 100 89 Ppat_XP_001779265 100 Ppat_XP_001754130 Kfla_5215 99 Kfla_8997 Cvar_EFN52689 94 Cvar_EFN52690 93 Crei_XP_001696789 100 100 Crei_XP_001696788 100 Crei_XP_001694496 100 Vcar_XP_002955238 Vcar_XP_002955218 93 96 95 Vcar_XP_002955217 Crei_XP_001699931 100 100 Vcar_XP_002947869 Vcar_XP_002947064 p-NRT2_tblastn_Otau_NC_014435.1_155021-156448_frame1 100 100 Mpus_Micpu49583 Ehux_311732 100 98 Ehux_62811 100 Ehux_440685 100 Chsp_5066 100 Ehux_361445 Ehux_73160 Anid_3235 100 100 Aory_CADAORAT00006174 100 Anid_7526 100 Tmel_XP_002841190 Ncra_6351NCU07205 100 Fgra_CEF72344 100 Bade_1945 100 100 Bade_5343 100 100 Bade_5232 Opar_3451 Ccin_CC1G_07229 100 Umay_XP_759996 100 Gpro_131472 100 100 Gpro_57051 Spun_SPPG_01654 94 Rirr_30454 98 100 Rirr_46659 Uram_251407 98 100 Mver_08622 Alim_62548 100 66 Alim_120676 Sagg_81712 100 Aker_43858 100 100 Aker_60652 Clim_g5611 Pinf_XP_002903614 98 96 100 100 Hara_4352 Phal_2142 100 Pult_2696 100 100 Pult_12610 Alai_CCA24412 96 Pult_5693 100 98 Pinf_XP_002900552 Pult_12598 100 100 Pinf_XP_002900550 100 Pinf_XP_002900551 Sarc_SARC_08916 100 Cfra_4046T1 Bnat_41977 98 100 Bnat_55712 99 Bnat_47047 100 95 Bnat_48035 100 Bnat_29248 85 Bnat_47189 Aano_F0Y6A2 100 Aano_F0YL80 82 Esil_CBJ31728 100 Esil_CBJ31725 100 99 Esil_CBJ31726 99 Esil_CBJ31727 Ptri_XP_002180934 89 100 97 81 Ptri_XP_002184871 Tpse_XP_002287398 83 Tpse_XP_002288802 100 87 Tpse_XP_002295904 Ptri_XP_002177983 90 100 Ptri_XP_002178487 98 Toce_31243 Toce_10904 96 83 Ptri_XP_002185352 Vbra_21071 100 89 Vbra_3602 100 Vbra_691 Smin_016992_t1 Gsul_4935 100 Cmer_CMG018C 100 Pyez_15784_g3774 100 90 Ccri_T00009493001 Gthe_154872 Cpar_16401Contig10789 100 99 Cpar_675Contig10946 Cpar_10143Contig53034

0.5 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure available8 under aCC-BY-NC 4.0 International license.

EUKNR SUOX SUOX

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Oxidored_molyb Mo-co_dimer Cyt-b5 FAD_binding_6 NAD_binding_1 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure 9available under aCC-BY-NC 4.0 International license.

embryo-Ntab_464 100 embryo-Ntab_2612 94 embryo-Ntab_919 100 99 embryo-Ntab_1822 98 embryo-Acoe_015_00061 99 embryo-Mgut_mgv1a003340m 100 embryo-Atha_10060 embryo-Sbic_04g034160 100 embryo-Bdis_3g57990 97 embryo-Ppat_XP_001775824 100 98 embryo-Ppat_XP_001777025 94 84 embryo-Kfla_2615 embryo-Smoe_XP_002987413 100 chloro-Mpus_Micpu70828 100 chloro-Otau_XP_003081527 crypto-Gthe_81582 SARhete-Toce_15700 100 100 SARhete-Tpse_XP_002289265 SARhete-Ptri_XP_002180496 100 tBLASTn_SARhete-Aano_scaffold_5_95839-97332_frame3 89 hapto-Ehux_428968 16 100 82 hapto-Chsp_2401 80 SARhete-Ngad_10682 SARrhiz-Bnat_50588 81 SARhete-Esil_CBJ25514 62 chloro-Vcar_XP_002955216 100 100 100 chloro-Crei_XP_001696787 chloro-Cvar_EFN52613 93 62 rhodo-Ccri_T00003048001 98 rhodo-Pyez_1166_g159 glauco-Cpar_20981Contig26815 rhodo-Gsul_5197 UP000010473_1567 99 66 UP000003959_5969 69 UP000010382_649 66 UP000008204_3295 UP000001510_5218 76 UP000002384_1491 100 59 UP000008206_3750 46 UP000010481_217 UP000034681_2334 71 Taxonomy UP000002511_390 Alignment statistics UP000002483_187 (sequence names) 100 UP000010378_4492 89 Number of taxa: 61 37 UP000019325_1417 Haptophyta 92 91 UP000010381_2265 Alignment length: 501 83 UP000004344_487 Rhodophyta 84 UP000010474_1007 Chloroplastida Parsimony info. sites: 82.00% 100 77 UP000010384_3421 Rhizaria 94 UP000010476_2388 Missing data: 2.04% UP000010471_297 Alveolata UP000000737_1157 89 99 Stramenopiles 64 UP000027395_2048 UP000010367_5533 97 Amoebozoa Phylogenetic inference UP000010478_4726 100 UP000004532_2649 Holozoa 99 Maximium likelihood UP000010471_24 UP000001332_4247 Metazoa 97 97 1000 UFBoot replicates UP000010386_1786 Holomycota 100 UP000010385_475 LG+R5 UP000001938_2801 Others

0.2 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which CAMPEP_0168924354-Aureococcus_anophagefferens_Strain_CCMP1850 85 97CAMPEP_0168884780-Aureococcus_anophagefferens_Strain_CCMP1850 was not certified by peer review) is the author/funder, who has grantedtBLASTn_SARhete-Aano_scaffold_5_95839-97332_frame3 bioRxiv a license to display the preprint in perpetuity. It is made 100 CAMPEP_0168968142-Aureococcus_anophagefferens_Strain_CCMP1850 84 Supplementary ﬁgure 10 100CAMPEP_0168875934-Aureococcus_anophagefferens_Strain_CCMP1850 available under aCC-BY-NC100CAMPEP_0169057216-Aureococcus_anophagefferens_Strain_CCMP1850 4.0 International license. 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CAMPEP_0113310270-Corethron_hystrix_Strain_308 CAMPEP_0118636878-Bolidomonas_pacifica_Strain_CCMP_1866 99 hapto-Chsp_2401 100 CAMPEP_0115851638-Chrysochromulina_rotalis_Strain_UIO044 96 CAMPEP_0184259560-non_described_non_described_Strain_CCMP2097 100 CAMPEP_0184198014-non_described_non_described_Strain_CCMP2097 CAMPEP_0169969618-Pleurochrysis_carterae_Strain_CCMP645 100CAMPEP_0169933410-Pleurochrysis_carterae_Strain_CCMP645 100 CAMPEP_0169989428-Pleurochrysis_carterae_Strain_CCMP645 CAMPEP_0183378280-Coccolithus_pelagicus_ssp_braarudi_Strain_PLY182g CAMPEP_0170100840-Dinobryon_sp._Strain_UTEXLB2267 99 100 100CAMPEP_0170092758-Dinobryon_sp._Strain_UTEXLB2267 99 CAMPEP_0170058458-Dinobryon_sp._Strain_UTEXLB2267 100 CAMPEP_0119041950-Ochromonas_sp_Strain_CCMP1899 82 CAMPEP_0182419934-Mallomonas_Sp_Strain_CCMP3275 SARhete-Ngad_10682 CAMPEP_0185207612-Pavlova_sp._Strain_CCMP459 100 97 CAMPEP_0185162370-Pavlova_sp._Strain_CCMP459 100 CAMPEP_0180003550-non_described_non_described_Strain_CCMP_2436 98 CAMPEP_0119406528-Chrysoculter_rhomboideus_Strain_RCC1486 CAMPEP_0172618968-Pseudopedinella_elastica_Strain_CCMP716 96 CAMPEP_0197660318-Pelagodinium_beii_Strain_RCC1491 98 CAMPEP_0169577730-Bigelowiella_natans_Strain_CCMP1259 99 CAMPEP_0172100874-Rhodomonas_salina_Strain_CCMP131986 93CAMPEP_0169543146-Bigelowiella_natans_Strain_CCMP623 CAMPEP_0172244354-Bigelowiella_natans_Strain_CCMP1258.1 100SARrhiz-Bnat_50588 66 99 CAMPEP_0114184402-Bigelowiella_natans_Strain_CCMP_2755100 CAMPEP_0185214690-Bigelowiella_natans_Strain_CCMP1242 95 CAMPEP_0184487870-Norrisiella_sphaerica_Strain_BC52 CAMPEP_0114515468-Chlorarachnion_reptans_Strain_CCCM449 99 98 CAMPEP_0167800192-Lotharella_globosa_Strain_CCCM811 100 100CAMPEP_0114103544-Lotharella_globosa_Strain_LEX01 CAMPEP_0170200618-Lotharella_oceanica_Strain_CCMP622 100 89 CAMPEP_0118603388-Lotharella_amoebiformis_Strain_CCMP2058 86 CAMPEP_0167762978-Gymnochlora_sp._Strain_CCMP2014 CAMPEP_0197543446-Partenskyella_glossopodia_Strain_RCC365 CAMPEP_0116719476-Heterosigma_akashiwo_Strain_NB 90 100CAMPEP_0116591588-Heterosigma_akashiwo_Strain_CCMP3107 100 CAMPEP_0116698642-Heterosigma_akashiwo_Strain_NB 100 CAMPEP_0117833506-Chattonella_subsalsa_Strain_CCMP2191 81 SARhete-Esil_CBJ25514 CAMPEP_0202351340-Dunaliella_tertiolecta_Strain_CCMP1320 100 100 CAMPEP_0202340168-Dunaliella_tertiolecta_Strain_CCMP1320 100 CAMPEP_0119107536-Chlamydomonas_cf_sp_Strain_CCMP681 chloro-Vcar_XP_002955216 100 93 chloro-Crei_XP_001696787 CAMPEP_0119134166-Genus_nov._species_nov._Strain_RCC2339 94 CAMPEP_0182605970-Picochlorum_sp._Strain_RCC944 100 100 CAMPEP_0118798938-Picochlorum_oklahomensis_Strain_CCMP2329 chloro-Cvar_EFN52613 75 CAMPEP_0185831638-Erythrolobus_australicus_Strain_CCMP3124 100 100 100 CAMPEP_0185843834-Erythrolobus_madagascarensis_Strain_CCMP3276 100 CAMPEP_0182429078-Mallomonas_Sp_Strain_CCMP3275 100 CAMPEP_0184707442-Porphyridium_aerugineum_Strain_SAG_1380_2 CAMPEP_0174904276-Rhodella_maculata_Strain_CCMP736 93 CAMPEP_0183998852-Tetraselmis_striata_Strain_LANL1001 100 93 CAMPEP_0183956970-Tetraselmis_striata_Strain_LANL1001 100 CAMPEP_0177598114-Tetraselmis_sp._Strain_GSL018 99 CAMPEP_0117670198-Tetraselmis_astigmatica_Strain_CCMP880 rhodo-Ccri_T00003048001 99 rhodo-Pyez_1166_g159 100 CAMPEP_0184690212-Compsopogon_coeruleus_Strain_SAG_36.94 66 97 CAMPEP_0198366706-Madagascaria_erythrocladiodes_Strain_CCMP3234 rhodo-Gsul_5197 CAMPEP_0184752016-Rhodosorus_marinus_Strain_UTEX_LB_2760 99 100 100 CAMPEP_0113966224-Rhodosorus_marinus CAMPEP_0198725626-Unidentified_sp._Strain_CCMP1999 CAMPEP_0196653088-Cyanoptyche_gloeocystis_Strain_SAG4.97 99 100 CAMPEP_0196651456-Cyanoptyche_gloeocystis_Strain_SAG4.97 glauco-Cpar_20981Contig26815 CAMPEP_0116354112-Alexandrium_tamarense_Strain_CCMP1771 100 100CAMPEP_0196623516-Micromonas_sp._Strain_RCC472 100CAMPEP_0116501694-Alexandrium_tamarense_Strain_CCMP1771 CAMPEP_0203042998-Micromonas_pusilla_Strain_CCMP1723_ 100 100CAMPEP_0202984600-Micromonas_sp._Strain_RCC451 CAMPEP_0197082026-Micromonas_sp._Strain_NEPCC29 100 97 CAMPEP_0196616858-Micromonas_sp._Strain_NEPCC29 CAMPEP_0117636182-Micromonas_sp._Strain_CCMP2099 100 CAMPEP_0181146368-Micromonas_sp_Strain_CCMP1646 99 100 CAMPEP_0181378026-Mantoniella_antarctica_Strain_SL_175 100 CAMPEP_0198685714-Mantoniella_sp_Strain_CCMP1436 chloro-Mpus_Micpu70828 100 99 CAMPEP_0203024284-Micromonas_pusilla_Strain_RCC1614 CAMPEP_0179712844-Ostreococcus_mediterraneus_Strain_clade_D_RCC1107 100 100 CAMPEP_0179683624-Ostreococcus_mediterraneus_Strain_clade_D_RCC2573 100 100 CAMPEP_0179728372-Ostreococcus_lucimarinus_Strain_clade_A_BCC118000 chloro-Otau_XP_003081527 CAMPEP_0197172342-Bathycoccus_prasinos_Strain_CCMP1898 78 99 100CAMPEP_0179635612-Ostreococcus_prasinos_Strain_BCC99000 CAMPEP_0198481554-Bathycoccus_prasinos_Strain_RCC716 CAMPEP_0202891428-Chlamydomonas_chlamydogama_Strain_SAG_11_48b embryo-Ntab_464 100 100 embryo-Ntab_2612 100 embryo-Ntab_919 Alignment statistics 100 100 embryo-Ntab_1822 100 embryo-Acoe_015_00061 Number of taxa: 343 65 100 embryo-Mgut_mgv1a003340m 100 embryo-Atha_10060 embryo-Sbic_04g034160 Alignment length: 505 100 100 embryo-Bdis_3g57990 99 embryo-Smoe_XP_002987413 Parsimony info. sites: 91.1% embryo-Ppat_XP_001775824 100 100 embryo-Ppat_XP_001777025 98 Missing data: 1.92% 64 embryo-Kfla_2615 CAMPEP_0182912432-Nephroselmis_pyriformis_Strain_CCMP717 79 CAMPEP_0198239056-Unidentified_sp_Strain_CCMP2111 100 100 CAMPEP_0197475768-Genus_nov._species_nov._Strain_RCC998 CAMPEP_0113920364-Picocystis_salinarum Phylogenetic inference CAMPEP_0119205538-Pycnococcus_provasolii_Strain_RCC2336 66 100 54 CAMPEP_0198708476-Pycnococcus_provasolii_Strain_RCC733 CAMPEP_0183789022-Crustomastix_stigmata_Strain_CCMP3273 Maximium likelihood 49 CAMPEP_0198212628-Pyramimonas_sp._Strain_CCMP2087 97 100 100 CAMPEP_0118927452-Pyramimonas_obovata_Strain_CCMP722 CAMPEP_0196592104-Pyramimonas_amylifera_Strain_CCMP720 1000 UFBoot replicates CAMPEP_0196272158-Prasinococcus_capsulatus_Strain_CCMP1194 CAMPEP_0177699900-Rhodomonas_lens_Strain_RHODO LG+R8 100 100CAMPEP_0117023330-Tiarina_fusus_Strain_LIS 100 CAMPEP_0172107052-Rhodomonas_salina_Strain_CCMP1319 100 100 CAMPEP_0202819312-Rhodomonas_sp._Strain_CCMP768 100 CAMPEP_0181323412-Rhodomonas_abbreviata_Strain_Caron_Lab_Isolate CAMPEP_0177714652-Rhodomonas_lens_Strain_RHODO CAMPEP_0179389624-Myrionecta_rubra_Strain_CCMP2563 93 100 93 CAMPEP_0173106456-Geminigera_sp._Strain_Caron_Lab_Isolate 93 crypto-Gthe_81582 CAMPEP_0180152204-non_described_non_described_Strain_CCMP2293 100 45 CAMPEP_0180365136-non_described_non_described_Strain_CCMP2293 CAMPEP_0169456864-Hemiselmis_andersenii_Strain_CCMP1180 Taxonomy 88 100CAMPEP_0114151502-Hemiselmis_andersenii_Strain_CCMP644 100 87 CAMPEP_0172054152-Hemiselmis_andersenii_Strain_CCMP441 (euk_db seq. names) 100 CAMPEP_0173418444-Hemiselmis_rufescens_Strain_PCC563 CAMPEP_0173387438-Hemiselmis_virescens_Strain_PCC157 CAMPEP_0172211800-Cryptomonas_curvata_Strain_CCAP979_52 Haptophyta CAMPEP_0175911198-Goniomonas_pacifica_Strain_CCMP1869 UP000002483_187 100 UP000010378_4492 Rhodophyta 100 UP000019325_1417 100 100 UP000010381_2265 Chloroplastida 90 UP000004344_487 76 UP000010474_1007 Rhizaria 100 UP000010384_3421 98 UP000010476_2388 UP000010471_297 Alveolata UP000001332_4247 100 UP000010386_1786 99 Stramenopiles 51 UP000010385_475 99 82 UP000001938_2801 82 UP000010471_24 Amoebozoa UP000010478_4726 82 100 52 UP000004532_2649 Holozoa UP000002511_390 UP000000737_1157 100 73 UP000027395_2048 Metazoa 79 UP000010367_5533 UP000010473_1567 Holomycota 93 UP000003959_5969 67 54 UP000010382_649 66 Others (including 99 UP000008204_3295 UP000001510_5218 MMETSP) 97 UP000034681_2334 82 UP000010481_217 UP000002384_1491 100 UP000008206_3750

0.2 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Supplementary ﬁgure 11 fungi-Aory_CADAORAT00006175 100 100 fungi-Anid_7892 88 fungi-Tmel_XP_002841192 100 fungi-Ncra_4204NCU04720 99 fungi-Fgra_CEF76735 fungi-Opar_3131 100 100 fungi-Bade_5354 fungi-Ccin_CC1G_07228 89 73 fungi-Umay_XP_759995 fungi-Uram_177615 77 99 fungi-Mcir_Mucci2_73657 fungi-Rirr_3245 46 100 fungi-Rirr_250550 SARhete-Pinf_XP_002900554 100 96 SARhete-Pult_9450 Alignment statistics hzoa-Clim_g4940 44 Number of taxa: 44 fungi-Spun_SPPG_07925 83 49 fungi-Gpro_158697 Alignment length: 805 SARhete-Aker_101422 Parsimony info. sites: 79.6% 62 100 SARhete-Sagg_75322 Missing data: 1.30% 31 SARhete-Alim_86378 SARhete-Toce_16230 100 Phylogenetic inference 100 SARhete-Tpse_XP_002287665 Maximium likelihood 100 SARhete-Ptri_XP_002180792 1000 UFBoot replicates 72 100 SARhete-Aano_F0Y6U7 SARhete-Esil_CBJ31380 LG+R5 SARalve-Smin_036678_t1 100 92 SARalve-Smin_040143_t1 100 SARalve-Vbra_16973 SARalve-Vbra_1590 UP000001635_3015 Taxonomy 100 (sequence names) 98 UP000010796_2200 100 UP000005438_2929 Haptophyta 92 UP000000493_1397 Rhodophyta 82 UP000002534_491 UP000001847_1509 Chloroplastida 100 UP000004889_2868 Rhizaria 100 UP000001693_3753 Alveolata 82 100 UP000037921_2448 Stramenopiles UP000002566_4011 99 Amoebozoa 72 UP000000925_552 100 UP000004947_1252 Holozoa UP000004358_4856 Metazoa 100 UP000003087_3029 Holomycota Others

fungi-Aory_CADAORAT00006175 100 100 fungi-Anid_7892 84 fungi-Tmel_XP_002841192 100 fungi-Ncra_4204NCU04720 96 fungi-Fgra_CEF76735 fungi-Opar_3131 100 100 fungi-Bade_5354 fungi-Ccin_CC1G_07228 88 89 fungi-Umay_XP_759995 fungi-Uram_177615 99 fungi-Mcir_Mucci2_73657 49 fungi-Rirr_3245 89 100 fungi-Rirr_250550 Alignment statistics hzoa-Clim_g4940 50 Number of taxa: 44 fungi-Spun_SPPG_07925 50 Alignment length: 806 93 fungi-Gpro_158697 SARhete-Aker_101422 Parsimony info. sites: 79.80% 81 Missing data: 1.31% 98 SARhete-Sagg_75322 77 SARhete-Alim_86378 hzoa-Cfra_4044T1 Phylogenetic inference 53 100 hzoa-Sarc_SARC_08918 Maximium likelihood SARhete-Toce_16230 100 1000 UFBoot replicates 100 SARhete-Tpse_XP_002287665 LG+R5 100 SARhete-Ptri_XP_002180792 92 100 SARhete-Aano_F0Y6U7 SARhete-Esil_CBJ31380 SARalve-Smin_036678_t1 100 94 SARalve-Smin_040143_t1 100 SARalve-Vbra_16973 SARalve-Vbra_1590 UP000001635_3015 100 Taxonomy 96 UP000010796_2200 (sequence names) 98 UP000005438_2929 Haptophyta 93 UP000000493_1397 Rhodophyta 75 UP000002534_491 UP000001847_1509 Chloroplastida 100 UP000004889_2868 Rhizaria 100 UP000001693_3753 Alveolata 86 Stramenopiles 100 UP000037921_2448 Amoebozoa 99 UP000002566_4011 92 UP000000925_552 Holozoa 100 UP000004947_1252 Metazoa UP000004358_4856 Holomycota 100 UP000003087_3029 Others

embryo-Mgut_mgv1a004568m100 100embryo-Mgut_mgv1a005457m 100embryo-Mgut_mgv1a027122m embryo-Mgut_mgv1a023402m 76 100embryo-Mgut_mgv1a022931m 29 embryo-Mgut_mgv1a025664m embryo-Ntab_3789 89 100 embryo-Ntab_3446 embryo-Mgut_mgv1a004332m 93 100embryo-Atha_11637 100 embryo-Atha_18762 embryo-Atha_16968 98 100embryo-Atha_1756 100 embryo-Atha_30033 embryo-Mgut_mgv1a004788m 100 100embryo-Bdis_3g01290 74 embryo-Bdis_3g01277 75 embryo-Sbic_04g000970 embryo-Bdis_3g01270 100 100embryo-Bdis_3g01250 66 embryo-Sbic_04g001000 embryo-Acoe_030_00093 100embryo-Acoe_030_00092 92 100embryo-Mgut_mgv1a004977m 100 embryo-Mgut_mgv1a019058m 99 embryo-Mgut_mgv1a023971m 99 embryo-Atha_3537 embryo-Sbic_03g032310 96 100 embryo-Bdis_2g47640 embryo-Acoe_002_00061 100 embryo-Sbic_03g025300 100 100 embryo-Bdis_2g40740 embryo-Atha_25512 100 embryo-Mgut_mgv1a005636m100 100 100embryo-Mgut_mgv1a005911m embryo-Mgut_mgv1a006145m 99 embryo-Acoe_002_00060 100embryo-Mpol_8180 99embryo-Mpol_14273 99embryo-Mpol_15963 100embryo-Mpol_16082 99 embryo-Mpol_14780 99 embryo-Mpol_9278 embryo-Mpol_10920 99 100 embryo-Mpol_13200 embryo-Mpol_11433 100 100 100embryo-Mpol_6345 100 embryo-Mpol_17009 48 100 embryo-Mpol_10947 embryo-Mpol_13516 embryo-Smoe_XP_002966266 98 embryo-Smoe_XP_002993278 99 embryo-Ppat_XP_001785194 99 100embryo-Ppat_XP_001768210 96 embryo-Ppat_XP_001768212 embryo-Ppat_XP_001765331 100 embryo-Ppat_XP_001754049 99 embryo-Ppat_XP_001768801 77 100 embryo-Ppat_XP_001779265 100 embryo-Ppat_XP_001754130 embryo-Kfla_8997 98 embryo-Kfla_5215 chloro-Cvar_EFN52689 85 chloro-Cvar_EFN52690 88 100 chloro-Crei_XP_001696788 100 chloro-Crei_XP_001696789 100 chloro-Crei_XP_001694496 100 chloro-Vcar_XP_002955238 chloro-Vcar_XP_002955217 89 91 85 chloro-Vcar_XP_002955218 100 chloro-Crei_XP_001699931 100 chloro-Vcar_XP_002947869 chloro-Vcar_XP_002947064 chloro-Mpus_Micpu49583 100 100 p-NRT2_tblastn_chloro-Otau_NC_014435.1_155021-156448_frame1 100 hapto-Ehux_62811 94 hapto-Ehux_311732 100 hapto-Ehux_440685 91 hapto-Chsp_5066 100 hapto-Ehux_361445 hapto-Ehux_73160 100 fungi-Anid_3235 100 fungi-Aory_CADAORAT00006174 100 fungi-Anid_7526 100 fungi-Tmel_XP_002841190 fungi-Fgra_CEF72344 100 fungi-Ncra_6351NCU07205 100 99 fungi-Bade_5343 100 fungi-Bade_1945 100 100 fungi-Bade_5232 fungi-Opar_3451 fungi-Umay_XP_759996 100 fungi-Ccin_CC1G_07229 99 100 fungi-Gpro_131472 100 fungi-Gpro_57051 98 fungi-Spun_SPPG_01654 fungi-Rirr_46659 99 100 fungi-Rirr_30454 92 fungi-Uram_251407 100 fungi-Mver_08622 SARhete-Alim_62548 100 SARhete-Alim_120676 99 SARhete-Aker_60652 100 100 SARhete-Aker_43858 100 SARhete-Sagg_81712 hzoa-Clim_g5611 SARhete-Pinf_XP_002903614 99 73 100 100 SARhete-Hara_4352 100 SARhete-Phal_2142 SARhete-Pult_12610 100 100 SARhete-Pult_2696 SARhete-Alai_CCA24412 88 79 SARhete-Pult_12598 83 SARhete-Pinf_XP_002900552 100 SARhete-Pult_5693 100 SARhete-Pinf_XP_002900551 100 SARhete-Pinf_XP_002900550 hzoa-Cfra_4046T1 100 hzoa-Sarc_SARC_08916 100SARhete-Ptri_XP_002178487 97 63 SARhete-Ptri_XP_002177983 75 SARhete-Toce_31243 SARhete-Tpse_XP_002295904 73 100SARhete-Tpse_XP_002288802 SARhete-Ptri_XP_002180934 80 96 SARhete-Ptri_XP_002184871 98 SARhete-Tpse_XP_002287398 91 SARhete-Toce_10904 25 SARhete-Ptri_XP_002185352 100 SARhete-Esil_CBJ31728 99SARhete-Esil_CBJ31725 100SARhete-Esil_CBJ31727 83 73 SARhete-Esil_CBJ31726 94 SARrhiz-Bnat_48035 100SARrhiz-Bnat_47047 99 SARrhiz-Bnat_55712 96 100 SARrhiz-Bnat_41977 100 SARrhiz-Bnat_29248 62 SARrhiz-Bnat_47189 SARhete-Aano_F0YL80 Species-speciﬁc 94 99 SARhete-Aano_F0Y6A2 100 SARalve-Vbra_21071 99 SARalve-Vbra_3602 duplication 100 SARalve-Vbra_691 Taxonomy SARalve-Smin_016992_t1 rhodo-Cmer_CMG018C 100 rhodo-Gsul_4935 (sequence names) 100 rhodo-Ccri_T00009493001 90 100 rhodo-Pyez_15784_g3774 Alignment statistics crypto-Gthe_154872 Haptophyta 100 glauco-Cpar_675Contig10946 100 glauco-Cpar_16401Contig10789 Number of taxa: 183 glauco-Cpar_10143Contig53034 Rhodophyta 100 UP000001550_718 100 UP000006801_2573 98 UP000007507_2881 Chloroplastida Alignment length: 422 97 UP000037884_2074 UP000007127_2333 95 Rhizaria UP000033468_3229 Parsimony info. sites: 96.20% 91 71 UP000008707_804 72 UP000000239_2168 Alveolata 100 UP000033642_2416 97 UP000018258_1469 Missing data: 2.16% 99 100UP000027249_633 UP000006242_2222 Stramenopiles UP000031623_2421 UP000002028_1312 100 Amoebozoa 100 UP000009309_2498 75 100 UP000003586_3111 100 UP000011058_4290 UP000001822_2291 Holozoa Phylogenetic inference 98 100 UP000010796_1928 95 100 UP000001635_3019 Metazoa UP000006073_2635 Maximium likelihood UP000001847_1514 100 66 100 UP000003087_3028 Holomycota 100 UP000010798_5465 99 UP000005943_1948 1000 UFBoot replicates UP000002221_1430 Others UP000008634_1772 92 UP000008898_1745 100 UP000004690_2917 LG+F+R8 100 UP000003919_1098

CAMPEP_0113471844-Nitzschia_sp 100 CAMPEP_0113522778-Nitzschia_sp 96 CAMPEP_0113621062-Cylindrotheca_closterium 100 92 CAMPEP_0113629350-Cylindrotheca_closterium CAMPEP_0172473460-Amphiprora_paludosa_Strain_CCMP125 100 99 CAMPEP_0198139584-Entomoneis_sp_Strain_CCMP2396 CAMPEP_0117025596-Tiarina_fusus_Strain_LIS 98 CAMPEP_0119561328-Stauroneis_constricta_Strain_CCMP1120 86 CAMPEP_0168745444-Amphiprora_sp_Strain_CCMP467 54 100CAMPEP_0168762414-Amphiprora_sp_Strain_CCMP467 100 CAMPEP_0168801944-Amphiprora_sp_Strain_CCMP467 75 100 CAMPEP_0172450178-Amphiprora_paludosa_Strain_CCMP125 CAMPEP_0198142418-Entomoneis_sp_Strain_CCMP2396 CAMPEP_0168778008-Amphiprora_sp_Strain_CCMP467 100 91 99 CAMPEP_0168814774-Amphiprora_sp_Strain_CCMP467 CAMPEP_0198138328-Entomoneis_sp_Strain_CCMP2396 SARhete-Ptri_XP_002178487 100 86 SARhete-Ptri_XP_002177983 CAMPEP_0170666546-Amphora_coffeaeformis_Strain_CCMP127 CAMPEP_0172375310-Pseudo_nitzschia_pungens_Strain_cf_cingulata 100 70 CAMPEP_0172384442-Pseudo_nitzschia_pungens_Strain_cf_pungens CAMPEP_0201146734-Pseudo_nitzschia_fraudulenta_Strain_WWA7 94 69 CAMPEP_0116096112-Pseudo_nitzschia_delicatissima_Strain_B596 99 100 100 CAMPEP_0197265694-Pseudo_nitzschia_delicatissima_Strain_UNC1205 CAMPEP_0116118036-Pseudo_nitzschia_arenysensis_Strain_B593 CAMPEP_0197186432-Pseudo_nitzschia_heimii_Strain_UNC1101 100 CAMPEP_0172370188-Pseudo_nitzschia_pungens_Strain_cf_cingulata 100 99 CAMPEP_0172387216-Pseudo_nitzschia_pungens_Strain_cf_pungens 100 CAMPEP_0116090704-Pseudo_nitzschia_delicatissima_Strain_B596 CAMPEP_0172400066-Pseudo_nitzschia_pungens_Strain_cf_pungens 81 100 99 CAMPEP_0197175954-Pseudo_nitzschia_heimii_Strain_UNC1101 CAMPEP_0113469460-Nitzschia_sp 100 100CAMPEP_0113506026-Nitzschia_sp 100 CAMPEP_0113482712-Nitzschia_sp CAMPEP_0178793146-Nitzschia_punctata_Strain_CCMP561 CAMPEP_0113614238-Cylindrotheca_closterium 100 46 CAMPEP_0113652532-Cylindrotheca_closterium 99 CAMPEP_0202447140-Licmophora_paradoxa_Strain_CCMP2313 100 CAMPEP_0195286136-Asterionellopsis_glacialis_Strain_CCMP134 CAMPEP_0170278972-Durinskia_baltica_Strain_CSIRO_CS_38 88 100 100CAMPEP_0170363224-Durinskia_baltica_Strain_CSIRO_CS_38 86 CAMPEP_0170208388-Durinskia_baltica_Strain_CSIRO_CS_38 45 CAMPEP_0170201166-Durinskia_baltica_Strain_CSIRO_CS_38 56 CAMPEP_0116550466-Cyclophora_tenuis_Strain_ECT3854 CAMPEP_0116847872-Astrosyne_radiata_Strain_13vi08_1A CAMPEP_0113570120-Odontella 91 89 CAMPEP_0180930090-Ditylum_brightwellii_Strain_Pop1_SS4 CAMPEP_0202480246-Staurosira_complex_sp_Strain_CCMP2646 95 CAMPEP_0178697866-Extubocellulus_spinifer_Strain_CCMP396 100 99CAMPEP_0178704536-Extubocellulus_spinifer_Strain_CCMP396 98CAMPEP_0178632526-Extubocellulus_spinifer_Strain_CCMP396 90 99CAMPEP_0178589758-Extubocellulus_spinifer_Strain_CCMP396 100 CAMPEP_0178541906-Extubocellulus_spinifer_Strain_CCMP396 CAMPEP_0181062662-Minutocellus_polymorphus_Strain_NH13 CAMPEP_0116006942-Leptocylindrus_danicus_var_danicus_Strain_B650 100 CAMPEP_0196804132-Leptocylindrus_danicus_Strain_CCMP1856 CAMPEP_0184832712-Thalassiosira_rotula_Strain_CCMP3096 69 85CAMPEP_0196162696-Thalassiosira_rotula_Strain_GSO102 100CAMPEP_0184800416-Thalassiosira_rotula_Strain_CCMP3096 97 CAMPEP_0201629482-Thalassiosira_gravida_Strain_GMp14c1 99CAMPEP_0184759892-Thalassiosira_rotula_Strain_CCMP3096 100 CAMPEP_0201627528-Thalassiosira_gravida_Strain_GMp14c1 100 CAMPEP_0172529754-Thalassiosira_punctigera_Strain_Tpunct2005C2 100 CAMPEP_0201951576-Thalassiosira_antarctica_Strain_CCMP982 CAMPEP_0183742926-Thalassiosira_miniscula_Strain_CCMP1093 100 96 CAMPEP_0183787716-Thalassiosira_miniscula_Strain_CCMP1093 100 CAMPEP_0181098600-Thalassiosira_sp_Strain_NH16 CAMPEP_0202136954-Thalassiosira_oceanica_Strain_CCMP1005 CAMPEP_0203363484-Thalassiosira_weissflogii_Strain_CCMP1010 89 62 CAMPEP_0203484014-Thalassiosira_weissflogii_Strain_CCMP1010 62 CAMPEP_0201860396-Thalassiosira_weissflogii_Strain_CCMP1010 93 7CAMPEP_0203198784-Thalassiosira_weissflogii_Strain_CCMP1010 94 6749CAMPEP_0203296800-Thalassiosira_weissflogii_Strain_CCMP1010 CAMPEP_0203259858-Thalassiosira_weissflogii_Strain_CCMP1010 100CAMPEP_0203104646-Thalassiosira_weissflogii_Strain_CCMP1010 92 CAMPEP_0201798838-Thalassiosira_weissflogii_Strain_CCMP1010 98 SARhete-Tpse_XP_002295904 100 100CAMPEP_0172353846-Thalassiosira_sp_Strain_FW SARhete-Tpse_XP_002288802 88 CAMPEP_0183761204-Thalassiosira_miniscula_Strain_CCMP1093 CAMPEP_0113388646-Skeletonema_costatum_Strain_1716 100 100CAMPEP_0115964252-Skeletonema_marinoi_Strain_SM1012Den_03 100CAMPEP_0197228532-Skeletonema_marinoi_Strain_UNC1201 100CAMPEP_0195177900-Skeletonema_dohrnii_Strain_SkelB 54 100 CAMPEP_0183698354-Skeletonema_menzelii_Strain_CCMP793 CAMPEP_0202271546-Thalassiosira_oceanica_Strain_CCMP1005 CAMPEP_0195353856-Chaetoceros_neogracile_Strain_CCMP1317 100 27 100 CAMPEP_0195388202-Chaetoceros_neogracile_Strain_CCMP1317 25 60 CAMPEP_0203718312-Chaetoceros_affinis_Strain_CCMP159 27 CAMPEP_0198250286-Chaetoceros_dichaeta_Strain_CCMP1751 CAMPEP_0197840110-Eucampia_antarctica_Strain_CCMP1452 CAMPEP_0113548808-Odontella CAMPEP_0113489762-Nitzschia_sp 61 99CAMPEP_0113509538-Nitzschia_sp 100CAMPEP_0113467914-Nitzschia_sp 100 CAMPEP_0113461208-Nitzschia_sp CAMPEP_0178745854-Nitzschia_punctata_Strain_CCMP561 100 100 CAMPEP_0178889838-Nitzschia_punctata_Strain_CCMP561 CAMPEP_0113610326-Cylindrotheca_closterium 99 31 CAMPEP_0116999848-Tiarina_fusus_Strain_LIS CAMPEP_0119552410-Stauroneis_constricta_Strain_CCMP1120 SARhete-Ptri_XP_002184871 100 40 CAMPEP_0202474104-Licmophora_paradoxa_Strain_CCMP2313 36 CAMPEP_0168837364-Amphiprora_sp_Strain_CCMP467 100 100 36 CAMPEP_0172439862-Amphiprora_paludosa_Strain_CCMP125 CAMPEP_0170660028-Amphora_coffeaeformis_Strain_CCMP127 100 97 CAMPEP_0170705086-Amphora_coffeaeformis_Strain_CCMP127 24 CAMPEP_0202486324-Staurosira_complex_sp_Strain_CCMP2646 SARhete-Ptri_XP_002180934 CAMPEP_0184766608-Thalassiosira_rotula_Strain_CCMP3096 CAMPEP_0184847796-Thalassiosira_rotula_Strain_CCMP3096 CAMPEP_0184812270-Thalassiosira_rotula_Strain_CCMP3096100 100CAMPEP_0184799488-Thalassiosira_rotula_Strain_CCMP3096 CAMPEP_0201656024-Thalassiosira_gravida_Strain_GMp14c1 100 100 CAMPEP_0201660262-Thalassiosira_gravida_Strain_GMp14c1 98 CAMPEP_0181128762-Thalassiosira_sp_Strain_NH16 SARhete-Tpse_XP_002287398 100 100 CAMPEP_0172347096-Thalassiosira_sp_Strain_FW CAMPEP_0172286322-Cyclotella_meneghiniana_Strain_CCMP_338 CAMPEP_0113608096-Cylindrotheca_closterium 82 100 CAMPEP_0195307922-Asterionellopsis_glacialis_Strain_CCMP134 100 CAMPEP_0178896132-Thalassionema_frauenfeldii_Strain_CCMP_1798 100 82 CAMPEP_0194238796-Thalassionema_nitzschioides_Strain_L26_B 100 CAMPEP_0119443014-Chaetoceros_cf_neogracile_Strain_RCC1993 100 90 89 CAMPEP_0176486822-Chaetoceros_sp_Strain_GSL56 CAMPEP_0198303250-Attheya_septentrionalis_Strain_CCMP2084 87 CAMPEP_0178943830-Rhizosolenia_setigera_Strain_CCMP_1694 CAMPEP_0180961314-Ditylum_brightwellii_Strain_Pop1_SS4 36 39 CAMPEP_0197833062-Eucampia_antarctica_Strain_CCMP1452 100 CAMPEP_0202509054-Staurosira_complex_sp_Strain_CCMP2646 100 CAMPEP_0194451012-Proboscia_alata_Strain_PI_D3 CAMPEP_0178940116-Rhizosolenia_setigera_Strain_CCMP_1694 CAMPEP_0168187172-Pseudo_nitzschia_australis_Strain_10249_10_AB 52 100CAMPEP_0168243042-Pseudo_nitzschia_australis_Strain_10249_10_AB 96 CAMPEP_0168243292-Pseudo_nitzschia_australis_Strain_10249_10_AB 89 CAMPEP_0201118370-Pseudo_nitzschia_fraudulenta_Strain_WWA7 91 100 CAMPEP_0197183452-Pseudo_nitzschia_heimii_Strain_UNC1101 99 CAMPEP_0170782856-Fragilariopsis_kerguelensis_Strain_L26_C5 99 CAMPEP_0194173390-Thalassiothrix_antarctica_Strain_L6_D1 95 CAMPEP_0194129108-Thalassiothrix_antarctica_Strain_L6_D1 99 CAMPEP_0119005792-Synedropsis_recta_cf_Strain_CCMP1620 99 CAMPEP_0195526092-Stephanopyxis_turris_Strain_CCMP_815 100 SARhete-Toce_31243 100 100 CAMPEP_0201626384-Thalassiosira_gravida_Strain_GMp14c1 CAMPEP_0194206574-Thalassionema_nitzschioides_Strain_L26_B 99 CAMPEP_0172415644-Aulacoseira_subarctica_Strain_CCAP_1002_5 SARhete-Toce_10904 90 SARhete-Ptri_XP_002185352 CAMPEP_0182437288-Mallomonas_Sp_Strain_CCMP3275 100 CAMPEP_0182437980-Mallomonas_Sp_Strain_CCMP3275 27 CAMPEP_0116608228-Heterosigma_akashiwo_Strain_CCMP3107 100 CAMPEP_0179532948-Heterosigma_akashiwo_Strain_CCMP_452 100 CAMPEP_0116685862-Heterosigma_akashiwo_Strain_NB 100 99 CAMPEP_0116778454-Heterosigma_akashiwo_Strain_NB CAMPEP_0117802114-Chattonella_subsalsa_Strain_CCMP2191 99 100 100CAMPEP_0117816516-Chattonella_subsalsa_Strain_CCMP2191 CAMPEP_0117740850-Chattonella_subsalsa_Strain_CCMP2191 CAMPEP_0113936098-Fibrocapsa_japonica CAMPEP_0171617388-non_described_non_described_Strain_CCMP2098 100 92 CAMPEP_0171867274-non_described_non_described_Strain_CCMP2098 58CAMPEP_0171867950-non_described_non_described_Strain_CCMP2098 93CAMPEP_0171835800-non_described_non_described_Strain_CCMP2098 27 93 CAMPEP_0171641338-non_described_non_described_Strain_CCMP2098 CAMPEP_0171605702-non_described_non_described_Strain_CCMP2098 100 CAMPEP_0171623894-non_described_non_described_Strain_CCMP2098 100 CAMPEP_0171710076-non_described_non_described_Strain_CCMP2098 99 59CAMPEP_0171814028-non_described_non_described_Strain_CCMP2098 100CAMPEP_0171830512-non_described_non_described_Strain_CCMP2098 CAMPEP_0171882748-non_described_non_described_Strain_CCMP2098 96 SARhete-Aano_F0YL80 100 100 CAMPEP_0169041436-Aureococcus_anophagefferens_Strain_CCMP1850 CAMPEP_0119260076-Genus_nov_species_nov_Strain_RCC1024 100 CAMPEP_0118894508-Chrysoreinhardia_sp_Strain_CCMP3193 100 100 100 CAMPEP_0197348224-Aureoumbra_lagunensis_Strain_CCMP1510 79 CAMPEP_0197419750-hzoa-Sarcinochrysis_sp_Strain_CCMP770 SARhete-Aano_F0Y6A2 SARhete-Esil_CBJ31728 100 87 SARhete-Esil_CBJ31725 100 SARhete-Esil_CBJ31726 100 SARhete-Esil_CBJ31727 CAMPEP_0171452012-Vaucheria_litorea_Strain_CCMP2940 SARrhiz-Bnat_48035 100 100CAMPEP_0114195002-Bigelowiella_natans_Strain_CCMP_2755 100CAMPEP_0169554116-Bigelowiella_natans_Strain_CCMP623 99 SARrhiz-Bnat_47047 100 100 CAMPEP_0114207772-Bigelowiella_natans_Strain_CCMP_2755 CAMPEP_0114514974-Chlorarachnion_reptans_Strain_CCCM449 87 CAMPEP_0167785182-Lotharella_globosa_Strain_CCCM811 61 100CAMPEP_0167786576-Lotharella_globosa_Strain_CCCM811 83 CAMPEP_0114077904-Lotharella_globosa_Strain_LEX01 99 CAMPEP_0114090272-Lotharella_globosa_Strain_LEX01 SARrhiz-Bnat_41977 100 CAMPEP_0169552470-Bigelowiella_natans_Strain_CCMP623 99 100 100 SARrhiz-Bnat_55712 CAMPEP_0167822188-Lotharella_globosa_Strain_CCCM811 CAMPEP_0114089370-Lotharella_globosa_Strain_LEX01 CAMPEP_0118597540-Lotharella_amoebiformis_Strain_CCMP2058 100 CAMPEP_0118603360-Lotharella_amoebiformis_Strain_CCMP2058 100 99 CAMPEP_0184485424-Norrisiella_sphaerica_Strain_BC52 100 85 CAMPEP_0184489646-Norrisiella_sphaerica_Strain_BC52 85 CAMPEP_0118594434-Lotharella_amoebiformis_Strain_CCMP2058 CAMPEP_0167751598-Gymnochlora_sp_Strain_CCMP2014 42 100 95 CAMPEP_0167759124-Gymnochlora_sp_Strain_CCMP2014 97 SARrhiz-Bnat_29248 100 100 CAMPEP_0114182456-Bigelowiella_natans_Strain_CCMP_2755 100 100 CAMPEP_0167791008-Lotharella_globosa_Strain_CCCM811 CAMPEP_0167741384-Gymnochlora_sp_Strain_CCMP2014 CAMPEP_0197519580-Partenskyella_glossopodia_Strain_RCC365 SARrhiz-Bnat_47189 100 CAMPEP_0169580930-Bigelowiella_natans_Strain_CCMP1259 SARhete-Pinf_XP_002903614 100 100 SARhete-Hara_4352 100 SARhete-Phal_2142 SARhete-Pult_12610 100 100 SARhete-Pult_2696 SARhete-Alai_CCA24412 100 SARhete-Pult_5693 50 54 SARhete-Pinf_XP_002900552 100 SARhete-Pult_12598 99 SARhete-Pinf_XP_002900551 100 SARhete-Pinf_XP_002900550 59 hzoa-Cfra_4046T1 100 hzoa-Sarc_SARC_08916 fungi-Anid_3235 100 100 fungi-Aory_CADAORAT00006174 100 fungi-Anid_7526 100 fungi-Tmel_XP_002841190 fungi-Fgra_CEF72344 100 fungi-Ncra_6351NCU07205 100 fungi-Bade_5343 100 100 fungi-Bade_1945 100 100 fungi-Bade_5232 fungi-Opar_3451 fungi-Umay_XP_759996 100 fungi-Ccin_CC1G_07229 100 fungi-Rirr_46659 100 fungi-Rirr_30454 80 100 fungi-Uram_251407 100 99 fungi-Mver_08622 Alignment statistics fungi-Gpro_131472 100 91 100 fungi-Gpro_57051 fungi-Spun_SPPG_01654 SARhete-Aker_60652 100 Number of taxa: 497 SARhete-Aker_43858 99 SARhete-Alim_62548 100 100 SARhete-Alim_120676 99 SARhete-Sagg_81712 hzoa-Clim_g5611 Alignment length: 420 CAMPEP_0174320334-Eutreptiella_gymnastica_like_Strain_CCMP1594 100 100CAMPEP_0174377342-Eutreptiella_gymnastica_like_Strain_CCMP1594 100 CAMPEP_0174314556-Eutreptiella_gymnastica_like_Strain_CCMP1594 CAMPEP_0174308668-Eutreptiella_gymnastica_like_Strain_CCMP1594 100 Parsimony info. sites: 98.10% 100 CAMPEP_0174373514-Eutreptiella_gymnastica_like_Strain_CCMP1594 100 CAMPEP_0113772528-Eutreptiella_gymnastica CAMPEP_0113748916-Eutreptiella_gymnastica 100 99 CAMPEP_0174284488-Eutreptiella_gymnastica_like_Strain_CCMP1594 Missing data: 1.67% CAMPEP_0168369970-Protoceratium_reticulatum_Strain_CCCM_535__CCMP_1889 100 CAMPEP_0168378340-Protoceratium_reticulatum_Strain_CCCM_535__CCMP_1889 99 CAMPEP_0176531698-Amphidinium_carterae_Strain_CCMP1314 100 100 CAMPEP_0176612594-Amphidinium_carterae_Strain_CCMP1314 SARalve-Smin_016992_t1 100 SARalve-Vbra_21071 100 100CAMPEP_0184564322-Alveolata_sp_Strain_CCMP3155 99 SARalve-Vbra_3602 SARalve-Vbra_691 Phylogenetic inference 100 100 CAMPEP_0184593174-Alveolata_sp_Strain_CCMP3155 CAMPEP_0180043234-non_described_non_described_Strain_CCMP_2436 100 100 CAMPEP_0180079524-non_described_non_described_Strain_CCMP_2436 100 CAMPEP_0179922358-non_described_non_described_Strain_CCMP_2436 Maximium likelihood CAMPEP_0185186900-Pavlova_sp_Strain_CCMP459 CAMPEP_0185829274-Erythrolobus_australicus_Strain_CCMP3124 100 100 CAMPEP_0185856472-Erythrolobus_madagascarensis_Strain_CCMP3276 59 CAMPEP_0182451574-Timspurckia_oligopyrenoides_Strain_CCMP3278 1000 UFBoot replicates 79 rhodo-Cmer_CMG018C 100 CAMPEP_0113954010-Rhodosorus_marinus 100 100 CAMPEP_0184738162-Rhodosorus_marinus_Strain_UTEX_LB_2760 93 CAMPEP_0198724398-Unidentified_sp_Strain_CCMP1999 CAMPEP_0174913806-Rhodella_maculata_Strain_CCMP736 LG+F+R10 16 100 CAMPEP_0184715032-Rhodella_maculata_Strain_CCMP_736 100 CAMPEP_0198309874-Madagascaria_erythrocladiodes_Strain_CCMP3234 rhodo-Ccri_T00009493001 100 94 rhodo-Pyez_15784_g3774 21 rhodo-Gsul_4935 crypto-Gthe_154872 embryo-Mgut_mgv1a004568m 100 100embryo-Mgut_mgv1a005457m 100embryo-Mgut_mgv1a027122m embryo-Mgut_mgv1a023402m 100 27 embryo-Mgut_mgv1a022931m 26 embryo-Mgut_mgv1a025664m 97 embryo-Mgut_mgv1a004332m embryo-Ntab_3789 100 embryo-Ntab_3446 Taxonomy 98 embryo-Atha_11637 100 100 embryo-Atha_18762 embryo-Atha_16968 99 embryo-Atha_1756 (euk_db seq. names) 100 100 embryo-Atha_30033 embryo-Mgut_mgv1a004788m 100 embryo-Bdis_3g01290 100 42 embryo-Bdis_3g01277 43 embryo-Sbic_04g000970 embryo-Bdis_3g01270 Haptophyta 100 100 embryo-Bdis_3g01250 29 embryo-Sbic_04g001000 embryo-Acoe_030_00093 100 embryo-Acoe_030_00092 Rhodophyta 91 embryo-Mgut_mgv1a004977m 100 100 embryo-Mgut_mgv1a019058m 99 embryo-Mgut_mgv1a023971m 100 embryo-Atha_3537 Chloroplastida embryo-Sbic_03g032310 100 99 embryo-Bdis_2g47640 embryo-Acoe_002_00061 embryo-Sbic_03g025300 100 Rhizaria 100 100 embryo-Bdis_2g40740 embryo-Atha_25512 100 embryo-Mgut_mgv1a005636m 100 100 100embryo-Mgut_mgv1a005911m embryo-Mgut_mgv1a006145m Alveolata 100 embryo-Acoe_002_00060 embryo-Mpol_8180 100 96embryo-Mpol_14273 96embryo-Mpol_15963 Stramenopiles 100embryo-Mpol_16082 100 embryo-Mpol_14780 100 embryo-Mpol_9278 embryo-Mpol_10920 100 Amoebozoa 100 embryo-Mpol_13200 embryo-Mpol_11433 100 100 embryo-Mpol_6345 100 100 embryo-Mpol_17009 Holozoa 27 100 embryo-Mpol_10947 embryo-Mpol_13516 embryo-Smoe_XP_002966266 99 embryo-Smoe_XP_002993278 embryo-Ppat_XP_001754049 100 Metazoa embryo-Ppat_XP_001768801 95 100 embryo-Ppat_XP_001779265 100 86 embryo-Ppat_XP_001754130 embryo-Ppat_XP_001765331 Holomycota 100 embryo-Ppat_XP_001785194 99 100embryo-Ppat_XP_001768210 embryo-Ppat_XP_001768212 p-NRT2_Leptophrysvorax_TRINITY_DN26206_c0_g3_i1_358-1494_frame1_0-codonstops 95 Others (including embryo-Kfla_8997 99 chloro-Crei_XP_001696788 100 100 chloro-Crei_XP_001696789 MMETSP) 75 97 chloro-Crei_XP_001694496 100 chloro-Vcar_XP_002955238 chloro-Vcar_XP_002955217 100 60 chloro-Vcar_XP_002955218 99 CAMPEP_0119102732-Chlamydomonas_cf_sp_Strain_CCMP681 CAMPEP_0202902966-Chlamydomonas_chlamydogama_Strain_SAG_11_48b 73 chloro-Crei_XP_001699931 100 59 100 chloro-Vcar_XP_002947869 89 chloro-Vcar_XP_002947064 CAMPEP_0202344034-Dunaliella_tertiolecta_Strain_CCMP1320 100 90 CAMPEP_0202344068-Dunaliella_tertiolecta_Strain_CCMP1320 CAMPEP_0118807540-Picochlorum_oklahomensis_Strain_CCMP2329 100 100 CAMPEP_0182618756-Picochlorum_sp_Strain_RCC944 90 chloro-Cvar_EFN52690 chloro-Cvar_EFN52689 embryo-Kfla_5215 CAMPEP_0114257736-Pyramimonas_parkeae_CCMP726 100 100CAMPEP_0114259088-Pyramimonas_parkeae_CCMP726 100 CAMPEP_0114310882-Pyramimonas_parkeae_Strain_CCMP726 100 CAMPEP_0114308706-Pyramimonas_parkeae_Strain_CCMP726 100 CAMPEP_0196585020-Pyramimonas_amylifera_Strain_CCMP720 98 CAMPEP_0118929966-Pyramimonas_obovata_Strain_CCMP722 CAMPEP_0170132788-Dolichomastix_tenuilepis_Strain_CCMP3274 100 CAMPEP_0183792002-Crustomastix_stigmata_Strain_CCMP3273 CAMPEP_0183851796-Tetraselmis_striata_Strain_LANL1001 96 100 100CAMPEP_0183956100-Tetraselmis_striata_Strain_LANL1001 99 CAMPEP_0183839258-Tetraselmis_striata_Strain_LANL1001 CAMPEP_0117675006-Tetraselmis_astigmatica_Strain_CCMP880 100 CAMPEP_0177758268-Tetraselmis_chuii_Strain_PLY429 72 96 CAMPEP_0177768568-Tetraselmis_chuii_Strain_PLY429 96 CAMPEP_0177783458-Tetraselmis_chuii_Strain_PLY429 100 CAMPEP_0177796714-Tetraselmis_chuii_Strain_PLY429 CAMPEP_0197489770-Genus_nov_species_nov_Strain_RCC856 86 94 100CAMPEP_0198446360-Unidentified_sp_Strain_RCC701 100 CAMPEP_0198643036-Phaeocystis_cordata_Strain_RCC1383 100 CAMPEP_0197471158-Genus_nov_species_nov_Strain_RCC998 CAMPEP_0197509678-Genus_nov_species_nov_Strain_RCC2335 100 100 CAMPEP_0198468794-Unidentified_sp_Strain_RCC1871 CAMPEP_0198235280-Unidentified_sp_Strain_CCMP2111 99 100 100 CAMPEP_0198246822-Unidentified_sp_Strain_CCMP2111 CAMPEP_0198247250-Unidentified_sp_Strain_CCMP2111 96 CAMPEP_0183826184-Picocystis_salinarum_Strain_CCMP1897 CAMPEP_0119156364-Genus_nov_species_nov_Strain_RCC2339 68 87 CAMPEP_0119179646-Prasinoderma_singularis_Strain_RCC927 CAMPEP_0182912314-Nephroselmis_pyriformis_Strain_CCMP717 CAMPEP_0181361844-Mantoniella_antarctica_Strain_SL_175 100 100CAMPEP_0181362120-Mantoniella_antarctica_Strain_SL_175 98CAMPEP_0198703650-Mantoniella_sp_Strain_CCMP1436 95 CAMPEP_0198702554-Mantoniella_sp_Strain_CCMP1436 94 CAMPEP_0198678930-Mantoniella_sp_Strain_CCMP1436 86 CAMPEP_0197595968-Genus_nov_species_nov_Strain_RCC2288 CAMPEP_0116366546-Alexandrium_tamarense_Strain_CCMP1771 98 100 100CAMPEP_0196619100-Micromonas_sp_Strain_RCC472 100CAMPEP_0196616784-Micromonas_sp_Strain_NEPCC29 CAMPEP_0202998822-Micromonas_sp_Strain_RCC451 100 99 CAMPEP_0203056734-Micromonas_pusilla_Strain_CCMP1723_ chloro-Mpus_Micpu49583 100 CAMPEP_0116463016-Alexandrium_tamarense_Strain_CCMP1771 100 78 78 CAMPEP_0116364978-Alexandrium_tamarense_Strain_CCMP1771 78 CAMPEP_0203000774-Micromonas_pusilla_Strain_CCAC1681 CAMPEP_0117623856-Micromonas_sp_Strain_CCMP2099 CAMPEP_0179742598-Ostreococcus_lucimarinus_Strain_clade_A_BCC118000 100 100 100CAMPEP_0181708040-Symbiodinium_sp_Strain_CCMP2430 100CAMPEP_0179728432-Ostreococcus_lucimarinus_Strain_clade_A_BCC118000 100CAMPEP_0181633792-Symbiodinium_sp_Strain_CCMP2430 91 CAMPEP_0181713006-Symbiodinium_sp_Strain_CCMP2430 89 84 100 CAMPEP_0179728352-Ostreococcus_lucimarinus_Strain_clade_A_BCC118000 100 p-NRT2_tblastn_chloro-Otau_NC_014435.1_155021-156448_frame1 99 CAMPEP_0198229398-Pyramimonas_sp_Strain_CCMP2087 CAMPEP_0197171802-Bathycoccus_prasinos_Strain_CCMP1898 100 CAMPEP_0198485408-Bathycoccus_prasinos_Strain_RCC716 CAMPEP_0119186116-Prasinoderma_singularis_Strain_RCC927 CAMPEP_0202776470-Isochrysis_sp_Strain_CCMP1244 CAMPEP_0196681708-Isochrysis_sp_Strain_CCMP1244100 100 CAMPEP_0196333756-Emiliania_huxleyi_Strain_379 hapto-Ehux_361445 100 100 CAMPEP_0181922060-Emiliania_huxleyi_Strain_PLY_M219 CAMPEP_0119300830-Scyphosphaera_apsteinii_Strain_RCC1455 91 CAMPEP_0118819248-Phaeocystis_Sp_Strain_CCMP2710 100 CAMPEP_0172991704-Phaeocystis_antarctica_Strain_Caron_Lab_Isolate 100 CAMPEP_0119098962-Undescribed_Undescribed_Strain_CCMP2000 100 74 CAMPEP_0172971330-Phaeocystis_antarctica_Strain_Caron_Lab_Isolate CAMPEP_0172952548-Phaeocystis_antarctica_Strain_Caron_Lab_Isolate 100 100 CAMPEP_0198192842-Phaeocystis_antarctica_Strain_CCMP1374 94 93 CAMPEP_0118825368-Phaeocystis_Sp_Strain_CCMP2710 CAMPEP_0174724824-Chrysochromulina_brevifilum_Strain_UTEX_LB_985 CAMPEP_0118816668-Phaeocystis_Sp_Strain_CCMP2710 100 CAMPEP_0183355456-Coccolithus_pelagicus_ssp_braarudi_Strain_PLY182g CAMPEP_0179754226-Isochrysis_galbana_Strain_CCMP1323 95 100 100 CAMPEP_0179773808-Isochrysis_galbana_Strain_CCMP1323 100 CAMPEP_0183619112-Isochrysis_galbana_Strain_CCMP_1323 93 99 CAMPEP_0185060940-Isochrysis_sp_Strain_CCMP1324 hapto-Ehux_62811 100 100 hapto-Ehux_311732 hapto-Ehux_440685 100 94 CAMPEP_0202744342-Isochrysis_sp_Strain_CCMP1244 100 hapto-Chsp_5066 CAMPEP_0182095296-Emiliania_huxleyi_Strain_CCMP370 36 78CAMPEP_0196563820-Emiliania_huxleyi_Strain_374 55CAMPEP_0196294980-Emiliania_huxleyi_Strain_379 98hapto-Ehux_73160 99CAMPEP_0196452118-Emiliania_huxleyi_Strain_379 100CAMPEP_0181934452-Emiliania_huxleyi_Strain_PLY_M219 100 CAMPEP_0185432686-Gephyrocapsa_oceanica_Strain_RCC1303 100 CAMPEP_0119344446-Scyphosphaera_apsteinii_Strain_RCC1455 91 85 CAMPEP_0183117560-Chrysochromulina_polylepis_Strain_CCMP1757 CAMPEP_0119354036-Calcidiscus_leptoporus_Strain_RCC1130 CAMPEP_0118078572-Lingulodinium_polyedra_Strain_CCMP_1738 100 100CAMPEP_0118223622-Lingulodinium_polyedra_Strain_CCMP_1738 100 CAMPEP_0118312696-Lingulodinium_polyedra_Strain_CCMP_1738 CAMPEP_0172786626-Ceratium_fusus_Strain_PA161109 100 CAMPEP_0172834884-Ceratium_fusus_Strain_PA161109 CAMPEP_0198721370-Pycnococcus_provasolii_Strain_RCC733 100 CAMPEP_0119193490-Pycnococcus_provasolii_Strain_RCC2336 CAMPEP_0196654122-Cyanoptyche_gloeocystis_Strain_SAG497 100 100 CAMPEP_0196667570-Cyanoptyche_gloeocystis_Strain_SAG497 100 glauco-Cpar_675Contig10946 99 glauco-Cpar_16401Contig10789 glauco-Cpar_10143Contig53034 UP000001550_718 100 100 UP000006801_2573 100 UP000007507_2881 100 UP000037884_2074 UP000007127_2333 100 UP000033468_3229 UP000008707_804 100 85 85 UP000000239_2168 100 UP000033642_2416 UP000018258_1469 100 100 100 UP000027249_633 UP000006242_2222 83 UP000031623_2421 UP000003087_3028 100 100 UP000010798_5465 100 UP000005943_1948 UP000002221_1430 UP000002028_1312 90 100 100 UP000009309_2498 100 UP000003586_3111 99 UP000011058_4290 UP000001822_2291 98 UP000010796_1928 100 100 98 100 UP000001635_3019 UP000006073_2635 UP000001847_1514 UP000004690_2917 84 52 UP000003919_1098 100 UP000008898_1745 UP000008634_1772

C. limacisporum H1 Nucleariida Ichthyosporea Labyrinthulea Oomycota Opisthosporidia + + Ochrophyta Blastocladiomycota / TPmet/nrt2/euknr/NAD(P)H-nir Stramenopiles Alveolata Chytridiomycota genes present in cluster Fungi Holomycota Other Fungi Ancestral genes present but not clustered Stramenopiles Other Holozoa genes lost within the lineage Nk52+Sdes

Opisthokonta partial de-clustering within the lineage Awhi+Pgem clustering within the lineage Ihof+Apar + +

S. arctica Holozoa Teretosporea C. fragrantissima Ichthyosporea C. limacisporum

C. limacisporum H2 Labyrinthulea Nucleariida Oomycota Opisthosporidia + + Ochrophyta Blastocladiomycota / TPmet/nrt2/euknr/NAD(P)H-nir Stramenopiles Alveolata Chytridiomycota genes present in cluster Fungi Holomycota Other Fungi Oomycota genes present but not clustered Other Holozoa genes lost within the lineage Nk52+Sdes Opisthokonta partial de-clustering within the lineage Awhi+Pgem Ihof+Apar + + clustering within the lineage S. arctica Holozoa Teretosporea C. fragrantissima Ichthyosporea C. limacisporum

Ichthyosporea H3 + Labyrinthulea Nucleariida Oomycota Opisthosporidia + + Ochrophyta Blastocladiomycota / Stramenopiles TPmet/nrt2/euknr/NAD(P)H-nir Alveolata Chytridiomycota Fungi Holomycota Other Fungi genes present in cluster Labyrinthulea Other Holozoa genes present but not clustered Nk52+Sdes genes lost within the lineage Opisthokonta Awhi+Pgem partial de-clustering within the lineage Ihof+Apar clustering within the lineage S. arctica Holozoa + + Teretosporea C. fragrantissima Ichthyosporea C. limacisporum

H4 Labyrinthulea Nucleariida + Oomycota Opisthosporidia + + TPmet/nrt2/euknr/NAD(P)H-nir Ochrophyta Blastocladiomycota / Stramenopiles genes present in cluster Alveolata Chytridiomycota Fungi Holomycota Other Fungi genes present but not clustered Labyrinthulea Other Holozoa genes lost within the lineage Nk52+Sdes partial de-clustering within the lineage Opisthokonta Awhi+Pgem + + clustering within the lineage Ihof+Apar Holozoa Oomycota S. arctica Teretosporea C. fragrantissima Ichthyosporea C. limacisporum

H5 Labyrinthulea Nucleariida + Oomycota Opisthosporidia + + Ochrophyta Blastocladiomycota / TPmet/nrt2/euknr/NAD(P)H-nir Stramenopiles Alveolata Chytridiomycota genes present in cluster Fungi Labyrinthulea Holomycota Stramenopiles Other Fungi genes present but not clustered Other Holozoa genes lost within the lineage Nk52+Sdes

Opisthokonta partial de-clustering within the lineage Awhi+Pgem

Ihof+Apar + + clustering within the lineage Holozoa Oomycota S. arctica Teretosporea C. fragrantissima Ichthyosporea C. limacisporum Labyrinthulea

C. limacisporum H6 Labyrinthulea Nucleariida + Oomycota Opisthosporidia + + Ochrophyta Blastocladiomycota / TPmet/nrt2/euknr/NAD(P)H-nir Stramenopiles Alveolata Chytridiomycota genes present in cluster Fungi Holomycota Oomycota Other Fungi Stramenopiles genes present but not clustered Other Holozoa genes lost within the lineage Nk52+Sdes Opisthokonta partial de-clustering within the lineage Awhi+Pgem Ihof+Apar + + clustering within the lineage Holozoa Oomycota Oomycota S. arctica Teretosporea C. fragrantissima Ichthyosporea C. limacisporum bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which 100embryo-Mgut_mgv1a004568m was not certified by peer review) is the author/funder, who has100e mbryo-Mgut_mgv1a005457mgranted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure 16 100embryo-Mgut_mgv1a027122m embryo-Mgut_mgv1a023402m available under a31CC-BY-NC100embryo-Mgut_mgv1a022931m 4.0 International license. embryo-Ntab_3789 85 100 embryo-Ntab_3446 embryo-Mgut_mgv1a025664m 84 embryo-Mgut_mgv1a004332m 91 100embryo-Atha_11637 100 embryo-Atha_18762 embryo-Atha_16968 95 100embryo-Atha_1756 100 embryo-Atha_30033 100 embryo-Mgut_mgv1a004788m 100embryo-Bdis_3g01290 67 embryo-Bdis_3g01277 68 embryo-Sbic_04g000970 embryo-Bdis_3g01270 100 99 embryo-Bdis_3g01250 Taxonomy 63 embryo-Sbic_04g001000 embryo-Acoe_030_00093 100embryo-Acoe_030_00092 (sequence names) 91 100embryo-Mgut_mgv1a004977m 100 embryo-Mgut_mgv1a019058m 98 embryo-Mgut_mgv1a023971m Haptophyta 98 embryo-Atha_3537 embryo-Sbic_03g032310 95 100 embryo-Bdis_2g47640 embryo-Acoe_002_00061 Rhodophyta 67 100 embryo-Sbic_03g025300 100 99 embryo-Bdis_2g40740 embryo-Atha_25512 Chloroplastida 99 100embryo-Mgut_mgv1a005636m 100 100embryo-Mgut_mgv1a005911m Rhizaria embryo-Mgut_mgv1a006145m embryo-Acoe_002_00060 embryo-Smoe_XP_002966266 Alveolata 100 embryo-Smoe_XP_002993278 98 100embryo-Mpol_8180 97embryo-Mpol_14273 Stramenopiles 97embryo-Mpol_15963 100embryo-Mpol_16082 99 embryo-Mpol_14780 Amoebozoa 99 embryo-Mpol_9278 embryo-Mpol_10920 99 100 embryo-Mpol_13200 Holozoa embryo-Mpol_11433 100 100 100embryo-Mpol_6345 100 embryo-Mpol_17009 Metazoa 100 embryo-Mpol_10947 embryo-Mpol_13516 Holomycota 99 embryo-Ppat_XP_001785194 100embryo-Ppat_XP_001768210 99 92 embryo-Ppat_XP_001768212 embryo-Ppat_XP_001765331 Others 99 98 embryo-Ppat_XP_001754049 100 embryo-Ppat_XP_001768801 85 embryo-Ppat_XP_001779265 100 embryo-Ppat_XP_001754130 embryo-Kfla_8997 98 embryo-Kfla_5215 chloro-Cvar_EFN52689 89 chloro-Cvar_EFN52690 93 100 chloro-Crei_XP_001696788 100 chloro-Crei_XP_001696789 99 chloro-Crei_XP_001694496 100 chloro-Vcar_XP_002955238 chloro-Vcar_XP_002955217 90 95 91 chloro-Vcar_XP_002955218 100 chloro-Crei_XP_001699931 100 chloro-Vcar_XP_002947869 chloro-Vcar_XP_002947064 chloro-Mpus_Micpu49583 100 100 p-NRT2_tblastn_chloro-Otau_NC_014435.1_155021-156448_frame1 100 hapto-Ehux_62811 99 hapto-Ehux_311732 100 hapto-Ehux_440685 97 hapto-Chsp_5066 100 hapto-Ehux_361445 hapto-Ehux_73160 100 fungi-Anid_3235 100 fungi-Aory_CADAORAT00006174 100 fungi-Anid_7526 100 fungi-Tmel_XP_002841190 fungi-Fgra_CEF72344 Alignment statistics 100 fungi-Ncra_6351NCU07205 100 100 fungi-Bade_5343 100 fungi-Bade_1945 Number of taxa: 181 100 100 fungi-Bade_5232 fungi-Opar_3451 fungi-Umay_XP_759996 Alignment length: 424 100 fungi-Ccin_CC1G_07229 99 100 fungi-Gpro_131472 100 fungi-Gpro_57051 Parsimony info. sites: 96.20% 99 fungi-Spun_SPPG_01654 fungi-Rirr_46659 99 100 fungi-Rirr_30454 Missing data: 2.25% fungi-Uram_251407 69 100 fungi-Mver_08622 SARhete-Alim_62548 100 SARhete-Alim_120676 100 SARhete-Aker_60652 100 100 SARhete-Aker_43858 Phylogenetic inference 96 SARhete-Sagg_81712 hzoa-Clim_g5611 98 71 Maximium likelihood 100 SARhete-Pinf_XP_002903614 100 SARhete-Hara_4352 100 SARhete-Phal_2142 SARhete-Pult_12610 1000 UFBoot replicates 100 100 SARhete-Pult_2696 SARhete-Alai_CCA24412 LG+F+R8 100 100 SARhete-Pinf_XP_002900551 60 SARhete-Pinf_XP_002900550 62 SARhete-Pult_5693 100 SARhete-Pinf_XP_002900552 SARhete-Pult_12598 SARhete-Ptri_XP_002178487 100 SARhete-Ptri_XP_002177983 98 64 69 SARhete-Toce_31243 SARhete-Tpse_XP_002295904 72 100SARhete-Tpse_XP_002288802 SARhete-Ptri_XP_002180934 90 97 SARhete-Ptri_XP_002184871 99 SARhete-Tpse_XP_002287398 SARhete-Toce_10904 90 SARhete-Ptri_XP_002185352 82 SARhete-Esil_CBJ31728 100 99 100 SARhete-Esil_CBJ31725 99SARhete-Esil_CBJ31727 92 79 SARhete-Esil_CBJ31726 SARhete-Aano_F0YL80 96 99 SARhete-Aano_F0Y6A2 SARrhiz-Bnat_48035 100SARrhiz-Bnat_47047 100 SARrhiz-Bnat_55712 99 100 SARrhiz-Bnat_41977 100 SARrhiz-Bnat_29248 91 SARrhiz-Bnat_47189 100 SARalve-Vbra_21071 99 SARalve-Vbra_3602 100 SARalve-Vbra_691 SARalve-Smin_016992_t1 rhodo-Cmer_CMG018C 100 rhodo-Gsul_4935 100 rhodo-Ccri_T00009493001 96 100 rhodo-Pyez_15784_g3774 crypto-Gthe_154872 99 glauco-Cpar_675Contig10946 99 glauco-Cpar_16401Contig10789 glauco-Cpar_10143Contig53034 100 UP000001550_718 100 UP000006801_2573 99 UP000007507_2881 96 UP000037884_2074 UP000007127_2333 96 UP000033468_3229 84 82 UP000008707_804 82 UP000000239_2168 100 UP000033642_2416 98 UP000018258_1469 99 100 UP000027249_633 UP000006242_2222 UP000031623_2421 100 UP000002028_1312 100 UP000009309_2498 80 100 UP000003586_3111 99 UP000011058_4290 UP000001822_2291 96 100 UP000010796_1928 92 100 UP000001635_3019 UP000006073_2635 UP000001847_1514 100 62 100 UP000003087_3028 100 UP000010798_5465 99 UP000005943_1948 UP000002221_1430 UP000008634_1772 84 UP000008898_1745 100 UP000004690_2917 99 UP000003919_1098

0.3 embryo-Mgut_mgv1a004568m bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted100 October 29, 2018. The copyright holder for this preprint (which 100embryo-Mgut_mgv1a005457m embryo-Mgut_mgv1a027122m was not certified by peer review) is the author/funder, who has granted100 bioRxiv a license to display the preprint in perpetuity. It is made embryo-Mgut_mgv1a022931m 100 Supplementary ﬁgure available17 under aCC-BY-NC38 4.0 Internationalembryo-Mgut_mgv1a023402m license. embryo-Ntab_3446 100 86 embryo-Ntab_3789 embryo-Mgut_mgv1a025664m 72 embryo-Mgut_mgv1a004332m 88 embryo-Atha_30033 100 100 embryo-Atha_1756 embryo-Mgut_mgv1a004788m 98 embryo-Atha_18762 100 100 embryo-Atha_11637 embryo-Atha_16968 100 embryo-Bdis_3g01290 100 66 embryo-Bdis_3g01277 embryo-Sbic_04g000970 69 embryo-Bdis_3g01250 99 100 embryo-Bdis_3g01270 61 embryo-Sbic_04g001000 embryo-Acoe_030_00092 100 embryo-Acoe_030_00093 81 embryo-Mgut_mgv1a004977m 100 100 embryo-Mgut_mgv1a019058m 98 embryo-Mgut_mgv1a023971m 96 embryo-Atha_3537 embryo-Bdis_2g47640 100 92 embryo-Sbic_03g032310 embryo-Acoe_002_00061 embryo-Mgut_mgv1a005636m 100 100 100embryo-Mgut_mgv1a005911m embryo-Mgut_mgv1a006145m 100 embryo-Sbic_03g025300 100 100 99 embryo-Bdis_2g40740 embryo-Atha_25512 98 embryo-Acoe_002_00060 embryo-Mpol_14273 100 100embryo-Mpol_8180 100embryo-Mpol_15963 100embryo-Mpol_16082 100 embryo-Mpol_14780 99 embryo-Mpol_9278 embryo-Mpol_13200 100 99 embryo-Mpol_10920 embryo-Mpol_11433 100 100 embryo-Mpol_17009 100 100 embryo-Mpol_6345 34 100 embryo-Mpol_10947 embryo-Mpol_13516 embryo-Smoe_XP_002993278 99 embryo-Smoe_XP_002966266 embryo-Ppat_XP_001768210 98 99 100 embryo-Ppat_XP_001785194 90 embryo-Ppat_XP_001768212 embryo-Ppat_XP_001765331 100 embryo-Ppat_XP_001779265 100 embryo-Ppat_XP_001754130 100 86 embryo-Ppat_XP_001768801 98 embryo-Ppat_XP_001754049 embryo-Kfla_5215 98 embryo-Kfla_8997 chloro-Cvar_EFN52690 93 chloro-Cvar_EFN52689 97 chloro-Crei_XP_001696788 100 100 chloro-Crei_XP_001696789 99 chloro-Crei_XP_001694496 100 chloro-Vcar_XP_002955238 chloro-Vcar_XP_002955217 95 93 94 chloro-Vcar_XP_002955218 chloro-Crei_XP_001699931 100 100 chloro-Vcar_XP_002947869 chloro-Vcar_XP_002947064 chloro-Mpus_Micpu49583 100 100 p-NRT2_tblastn_chloro-Otau_NC_014435.1_155021-156448_frame1 hapto-Ehux_311732 100 96 hapto-Ehux_62811 100 hapto-Ehux_440685 94 hapto-Chsp_5066 100 hapto-Ehux_361445 hapto-Ehux_73160 fungi-Aory_CADAORAT00006174 100 100 fungi-Anid_3235 100 fungi-Anid_7526 100 fungi-Tmel_XP_002841190 fungi-Fgra_CEF72344 100 fungi-Ncra_6351NCU07205 100 fungi-Bade_5343 100 100 fungi-Bade_1945 100 100 fungi-Bade_5232 fungi-Opar_3451 fungi-Ccin_CC1G_07229 100 fungi-Umay_XP_759996 99 fungi-Gpro_57051 100 100 fungi-Gpro_131472 fungi-Spun_SPPG_01654 61 fungi-Rirr_30454 98 99 fungi-Rirr_46659 fungi-Mver_08622 90 100 fungi-Uram_251407 SARhete-Aker_60652 100 SARhete-Aker_43858 99 98 SARhete-Alim_120676 100 100 SARhete-Alim_62548 99 SARhete-Sagg_81712 hzoa-Clim_g5611 SARhete-Tpse_XP_002288802 100 53 SARhete-Tpse_XP_002295904 SARhete-Toce_31243 66 SARhete-Ptri_XP_002177983 100 65 SARhete-Ptri_XP_002178487 58 SARhete-Ptri_XP_002185352 99 SARhete-Ptri_XP_002180934 61 91 SARhete-Ptri_XP_002184871 99 SARhete-Toce_10904 SARhete-Tpse_XP_002287398 SARhete-Esil_CBJ31727 79 97 SARhete-Esil_CBJ31726 100 SARhete-Esil_CBJ31725 100 72 SARhete-Esil_CBJ31728 SARhete-Aano_F0Y6A2 99 100 97 SARhete-Aano_F0YL80 90 SARrhiz-Bnat_41977 100 SARrhiz-Bnat_55712 98 SARrhiz-Bnat_47047 100 53 98 SARrhiz-Bnat_48035 100 SARrhiz-Bnat_29248 Taxonomy SARrhiz-Bnat_47189 hzoa-Sarc_SARC_08916 100 (sequence names) 94 hzoa-Cfra_4046T1 SARalve-Vbra_3602 100 Alignment statistics 99 SARalve-Vbra_21071 Haptophyta 100 SARalve-Vbra_691 Number of taxa: 172 SARalve-Smin_016992_t1 Rhodophyta rhodo-Gsul_4935 99 rhodo-Cmer_CMG018C Alignment length: 425 98 Chloroplastida rhodo-Ccri_T00009493001 100 89 rhodo-Pyez_15784_g3774 Rhizaria Parsimony info. sites: 96.20% crypto-Gthe_154872 glauco-Cpar_675Contig10946 Missing data: 2.22% 99 Alveolata 100 glauco-Cpar_16401Contig10789 glauco-Cpar_10143Contig53034 UP000009309_2498 Stramenopiles 100 100 UP000002028_1312 Phylogenetic inference 100 UP000003586_3111 Amoebozoa 100 UP000011058_4290 Maximium likelihood UP000001822_2291 Holozoa 98 UP000001635_3019 100 1000 UFBoot replicates 99 100 UP000010796_1928 Metazoa UP000006073_2635 UP000001847_1514 Holomycota LG+F+R7 69 UP000010798_5465 100 100 UP000003087_3028 Others 99 UP000005943_1948 UP000002221_1430 UP000006801_2573 100 100 UP000001550_718 100 UP000007507_2881 88 100 UP000037884_2074 UP000007127_2333 96 UP000033468_3229 UP000008707_804 96 82 83 UP000000239_2168 UP000033642_2416 100 100 UP000018258_1469 99 100 99 UP000027249_633 UP000006242_2222 UP000031623_2421 UP000003919_1098 100 UP000004690_2917 100 UP000008634_1772 95 UP000008898_1745

0.3 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure 18available under aCC-BY-NC 4.0 International license.

p-NaR_embryo-Ntab_1398 100 98 p-NaR_embryo-Ntab_3449 80 p-NaR_embryo-Mgut_mgv1a000999m p-NaR_embryo-Acoe_028_00143 100 93 p-NaR_embryo-Acoe_014_00164 p-NaR_embryo-Atha_23813 95 Taxonomy 89 p-NaR_embryo-Atha_4664 Alignment statistics p-NaR_embryo-Sbic_07g022750 (sequence names) 84 100 95 p-NaR_embryo-Sbic_04g024300 Number of taxa: 74 p-NaR_embryo-Bdis_3g37940 Haptophyta p-NaR_embryo-Sbic_04g034470 100 100 Alignment length: 378 p-NaR_embryo-Bdis_3g57680 Rhodophyta p-NaR_embryo-Smoe_XP_002972481 100 Chloroplastida 97 p-NaR_embryo-Smoe_XP_002984312 Parsimony info. sites: 89.20% p-NaR_embryo-Ppat_XP_001765828 100 Rhizaria 37 p-NaR_embryo-Ppat_XP_001762979 Missing data: 3.06% 84 92 p-NaR_embryo-Mpol_11980 Alveolata p-NaR_embryo-Mpol_4023 p-NaR_embryo-Kfla_13647 83 Stramenopiles p-NaR_SARhete-Aano_F0Y6U9 20 p-NaR_chloro-Crei_NaR Amoebozoa Phylogenetic inference 100 99 p-NaR_chloro-Vcar_XP_002955156 Holozoa 98 p-NaR_SARrhiz-Bnat_50585 Maximium likelihood 83 p-NaR_chloro-Cvar_EFN52691 Metazoa 49 p-NaR_hapto-Chsp_6322 1000 UFBoot replicates p-NaR_SARhete-Esil_CBN78746 Holomycota p-NaR_rhodo-Ccri_T00008899001 100 LG+R6 39 100 p-NaR_rhodo-Ccri_T00003369001 Others p-NaR_rhodo-Pyez_14599_g3505 38 p-NaR_SARhete-Tpse_XP_002294410 95 100 p-NaR_SARhete-Toce_9484 p-NaR_SARhete-Ptri_XP_002183599 60 p-NaR_SARhete-Sagg_102072 96 100 p-NaR_SARhete-Alim_120674 29 39 p-NaR_SARhete-Aker_39005 76 p-NaR_rhodo-Cmer_CMG019C 94 p-NaR_glauco-Cpar_30822Contig8487 p-NaR_SARhete-Sagg_70979 p-NaR_SARalve-Smin_039611_t1 100 84 p-NaR_SARalve-Smin_036677_t1 p-NaR_chloro-Mpus_Micpu57689 78 66 p-NaR_chloro-Otau_XP_003081526 97 58 61 p-NaR_chloro-Mpus_Micpu39565 p-NaR_SARhete-Ngad_6620 p-NaR_fungi-Spun_SPPG_02797 p-NaR_SARhete-Pinf_XP_002900553 100 p-NaR_SARhete-Pult_12566 95 p-NaR_hzoa-Sarc_SARC_08917 100 38 p-NaR_hzoa-Cfra_4045T1 p-NaR_fungi-Aory_CADAORAT00001983 100 87 p-NaR_fungi-Anid_4799 75 p-NaR_fungi-Gpro_95808 99 p-NaR_fungi-Spun_SPPG_02976 51 39 p-NaR_amoe-Acas_g4485 p-NaR_hzoa-Nk52_9149 31 p-NaR_fungi-Rirr_74537 100 76 p-NaR_fungi-Rirr_335331 p-NaR_fungi-Gpro_102987 p-NaR_fungi-Mver_08621 50 p-NaR_fungi-Tmel_XP_002841191 100 p-NaR_fungi-Anid_NaR 99 p-NaR_fungi-Ncra_4706NCU05298 100 100 p-NaR_fungi-Fgra_CEF74158 p-NaR_fungi-Bade_5476 100 49 p-NaR_fungi-Bade_4998 100 100 p-NaR_fungi-Opar_4267 p-NaR_fungi-Ccin_CC1G_07230 100 100 p-NaR_fungi-Umay_XP_759994 p-NaR_fungi-Uram_251409 89 p-NaR_fungi-Mcir_Mucci2_81522 p-NaR_SARalve-Vbra_11175 P51687_SOX_anim-Hsap 100 100 Q9VWP4_SOX_Ecoli Q9S850_SOX_embryo-Atha

0.3 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which Supplementarywas not certified by peer review)ﬁgure is the author/funder, 19 who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license.

0.968UP000001511_330 0.897 UP000010101_160 0.068UP000010474_2677 UP000002483_1432 0.7310.916UP000010378_545 0.787UP000010381_1245 UP000001191_5241 0.8310.822UP000010475_3685 UP000010390_3437 0.5870.807UP000019325_31 0.841 UP000004344_3807 UP000010384_1034 0.7450.095UP000010476_143 0.914 UP000010367_404 0.685 UP000010383_2964 0.876 UP000010472_219 0.681 UP000003959_4727 0.73 UP000010471_371 UP000003835_4752 0.999UP000001203_1732 0.317 UP000003922_1053 0.953 UP000031625_313 0.889 UP000008204_1800 0.921 0.842UP000002384_1001 0.7 0.748 UP000008206_2074 UP000001510_5433 UP000010481_3352 0.525 0.971UP000000737_1191 0.867 0.932 UP000033607_202 0.311 UP000006803_2089 UP000004532_1266 0.9130.945 UP000010478_2900 0.757 UP000008878_3009 0.229 UP000027395_2864 UP000010480_2995 0.281 UP000001332_3187 UP000001651_628 0.924 0.99 UP000013858_1015 0.711 UP000005766_968 0.828 UP000034681_1707 UP000001938_614 0.498 0.957 UP000000440_998 0.782 UP000002511_1986 UP000010379_2186 0.289 embryo-Mgut_mgv1a008675m 0.851 embryo-Atha_11552 0.775 0.994 embryo-Acoe_010_00582 embryo-Bdis_3g26680 0.871 0.983embryo-Sbic_01g022060 0.88 embryo-Kfla_2042 embryo-Mpol_12506 0.674 0.877 embryo-Ppat_XP_001753735 embryo-Smoe_XP_002977699 0.763 0.448 embryo-Smoe_XP_002979574 0.798 chloro-Cvar_EFN54442 0.997 0.964 chloro-Mpus_Micpu21165 chloro-Otau_XP_003082866 0.526 chloro-Vcar_XP_002949309 1 chloro-Crei_XP_001693738 UP000000671_7575 0.94 UP000002432_4723 UP000001258_3899 UP000002620_904 0.805 UP000008544_159 0.874 0.27 UP000000467_1790 0.2150.912 UP000037784_2700 UP000034222_3627 0.3470.34 UP000008289_1146 0.932 UP000006556_2387 0.707 UP000033493_1710 0.951 UP000013520_1228 0.855 UP000033439_1913 1 UP000004324_2993 0.9 UP000027983_3878 UP000001556_61 UP000017936_1494 0.739 UP000006919_1696 0.967 UP000018377_2126 0.554 0.724 UP000007054_183 0.367 UP000017924_411 UP000018385_1617 0.936 0.602 UP000018411_343 0.388 UP000018090_854 0.965 UP000003639_1020 0.433 0.919 UP000018011_1185 0.958UP000018021_1846 0.815 0.17 UP000018032_781 0.977 UP000018135_1883 UP000018333_1171 0.094 UP000005435_205 0.727UP000033115_4306 0.997 UP000002411_1897 0.663 UP000011728_4395 UP000007041_953 0.825 0.091 UP000017951_8 0.96 UP000018148_208 0.619 UP000018313_1348 UP000000719_1352 0.859 0.971 UP000000555_2465 0.186 0.231 UP000002156_177 UP000000272_616 UP000002706_2550 0.915UP000003730_1973 0.877UP000016160_201 0.828 UP000008297_1286 0.942 0.752UP000008634_1534 0.85 UP000008898_1686 0.815 0.94 UP000033681_2075 0.577 UP000023772_3195 0.456 UP000000493_606 0.992 UP000002011_5580 0.892 UP000002875_3817 0.922UP000017990_3293 0.993 0.954 UP000018063_1918 0.948UP000018199_1949 0.964 UP000034982_958 UP000008720_2926 UP000002221_256 UP000034509_574 0.948 UP000034897_300 0.866 UP000034181_683 0.409 UP000002574_1258 UP000019023_1056 0.648 0.36 UP000001369_900 0.643 UP000005496_2995 0.67 0.916 UP000007347_3004 0.795 UP000034504_266 0.643 UP000002587_57 UP000034674_824 UP000033912_236 0.88 UP000034682_643 0.294 UP000004793_1260 0.348 0.935 UP000017964_614 0.921 UP000034765_1020 UP000005392_887 0.658 0.316 UP000034626_787 0.155 0.901 UP000034749_524 0.908 UP000034328_18 UP000034569_341 0.664 UP000006055_491 0.404 UP000035036_622 0.888 UP000005695_703 0.538 0.623 UP000002534_1141 0.903 UP000001933_536 UP000002420_1800 0.968 UP000008825_1252 UP000033378_1849 0.953 UP000006793_1484 UP000006791_938 0.884 UP000006365_1352 0.441 UP000004664_1414 0.854 UP000006282_503 UP000000238_1150 0.165 UP000002171_273 0.767 UP000003544_369 0.731 0.554 UP000007077_3030 0.166 0.98 UP000011757_1310 0.241 UP000000998_2386 0.835 UP000002713_502 UP000034071_1754 0.907 1 UP000000579_1473 0.623 UP000001432_1320 0.955 UP000006859_2634 0.269 UP000033449_1759 UP000001171_2358 0.911 0.85 UP000001870_3384 0.843 UP000000547_612 0.804 UP000005870_2940 0.913UP000025222_3293 0.912 UP000008840_2189 0.899 0.699 UP000000812_2175 0.854 UP000001962_679 0.85 UP000031623_3036 UP000006838_2613 UP000033581_2118 0.878 UP000002793_21 0.949 hapto-Chsp_3869 0.856 hapto-Ehux_55801 0.848 crypto-Gthe_67488 SARhete-Esil_CBN74644 0.944 0.932 SARhete-Ngad_7772 SARalve-Vbra_14994 0.63 0.893 glauco-Cpar_10082Contig52972 rhodo-Cmer_CMT518C 0.854 0.84 SARhete-Aano_F0Y9H1 0.711 rhodo-Ccri_T00003703001 0.863 0.981 rhodo-Pyez_24683_g6087 SARhete-Bhom_1971 0.541 rhodo-Gsul_5142 SARalve-Ptet_A0CT60_A0CT60 0.789 1 SARalve-Ptet_A0DIL0_A0DIL0 0.988 SARalve-Tthe_XP_976860 0.998 0.961 SARalve-Imul_4538 0.886 0.925 SARalve-Otri_15614 0.603 UP000000788_776 0.985 UP000001115_511 UP000001026_879 exca-Ngru_XP_002681610 0exca-Linf_6381.929 0.807 0.744exca-Lmaj_XP_003722729 0.868exca-Lbra_1435 0.943exca-Lpyr_3037 0.912 exca-Lsey_3268 0.904exca-Tbru_EAN77132 0.987 0.477 exca-Tcru_10360 exca-Adea_EPY42868 0.994 exca-Bsal_BS64490 exca-Pesp_731 0.963UP000037774_446 0.916 UP000031523_5570 0.534 UP000004367_1751 0.622 UP000014417_1918 UP000002029_4778 0.828 0.982 0.922UP000000637_1252 0.835 0.999 UP000003828_226 UP000002007_2889 0.873 UP000005513_4414 0.138 UP000006011_925 0.962 UP000006762_3376 0.979 UP000031521_4376 0.75 0.56 UP000009381_953 UP000003947_3215 0.846 0.99 UP000005263_2465 0.87 UP000002526_7374 0.27 UP000002930_1379 0.843 UP000001399_3383 0.854 UP000001868_1541 0.956 UP000031368_246 UP000002480_189 0.999UP000008005_182 0.754 UP000028183_535 0.327 0.976 SARrhiz-Rfil_3774742_4s1f1 0.219 UP000037884_449 0.548 UP000004732_1086 UP000006639_1017 0.969UP000004510_404 0.793UP000006876_3005 0.507 0.869UP000002676_398 0.827UP000001225_834 UP000001977_260 0.7850.956UP000026398_4380 0.702 UP000005267_549 1UP000016497_595 0.9970.16 anim-Isca_XP_002414410 UP000008737_1136 0.903 UP000019805_242 0.998 UP000003612_1995 0.998 UP000004105_466 0.99 UP000000501_292 0.988 0.098 UP000034156_1009 0.911 UP000001625_1453 0.922 UP000015559_1846 UP000002742_2067 0.426 0.905UP000002743_1207 UP000002588_864 0.998 UP000013140_1100 SARalve-Smin_031902_t1 SARalve-Smin_031902_t2 UP000008457_2804 0.998embryo-Bdis_1g62230 0.776 embryo-Sbic_01g035110 0.868 embryo-Mgut_mgv1a011606m embryo-Acoe_007_00071 0.963 0.994embryo-Acoe_014_00501 0.048 embryo-Atha_10629 0.998embryo-Smoe_XP_002973080 0.9540.537 embryo-Smoe_XP_002976788 embryo-Mpol_7909 0.874 embryo-Ppat_XP_001782781 0.938 embryo-Kfla_5701 rhodo-Cmer_CMJ181C 0.791 0.918 chloro-Mpus_Micpu22456 amoe-Acas_g11520 0.957 apuso-Ttra_AMSG_05578 0.761hzoa-Sdes_comp18928_c1_seq1m9398 0.996hzoa-Sdes_comp18928_c1_seq3m9400 0.757 0.902 hzoa-Sdes_comp18928_c1_seq4m9402 0.925 hzoa-Nk52_3514 0.706 hzoa-Clim_g3543 anim-Hmag_XP_002154368 0.856 anim-Hrob_169662 SARrhiz-Bnat_39724 0.456 0.415 0.493 rhodo-Ccri_T00008650001 0.913 rhodo-Pyez_9426_g2263 0.678 crypto-Gthe_158589 0.903 0.999crypto-Gthe_49003 SARhete-Bhom_3644 0.864 hzoa-Cowc_CAOG_04356 amoe-Ddis_XP_643259 0.95amoe-Dpur_3044 1 amoe-Dfas_3524 0.638amoe-Ppal_EFA83547_1 exca-Scul_EPY20937 exca-Scul_EPY23976 exca-Scul_EPY29603 exca-Scul_EPY33275 0.843 exca-Scul_EPY35701 exca-Scul_EPY37065 0.712 exca-Phsp_CCW65616 0.184 0.969exca-Linf_5214 0.924exca-Lmaj_XP_001685147 exca-Lbra_7670 0.929exca-Lpyr_3662 0.232 0.386exca-Lsey_441 0.973 exca-Tbru_AAZ11055 0.951exca-Tcru_3163 exca-Adea_EPY35438 0.981 exca-Adea_EPY38403 0.993exca-Adea_EPY38306 exca-Adea_EPY42700 0.698 exca-Bsal_BS70875 0.897 0.99exca-Bsal_BS93920 0.741 anim-Odio_GSOIDT00007068001 0.927 exca-Mosp_12479 amoe-Ehis_129_m00136 0.962amoe-Enut_2508 1 Edis_493 amoe-Einv_4863 amoe-Einv_4969 chloro-Vcar_XP_002953211 0.983 chloro-Crei_XP_001702216 0.705 anim-Aque_15046 0.808 0.895 hmycota-Nspp_Unigene5324_16336 0.766 chloro-Cvar_EFN52147 rhodo-Gsul_2733 0.187 hzoa-Mvib_comp4545_c0_seq1_m2486 0.455fungi-Mcir_Mucci2_171142 0.626 0.973fungi-Rory_3234 0.93 fungi-Pbla_Phybl2_131104 0.767 fungi-Uram_258616 0.807 fungi-Mver_02400 0.824 fungi-Ccor_49231 0.111 fungi-Rirr_247874 fungi-Amac_01225 Taxonomy 0.994fungi-Amac_05414 0.749 fungi-Cang_54957 0.99 hzoa-Awhi_Unigene29430_m17960 0.904 hzoa-Pgem_Unigene3062_Pirum_gemmatam2093 0.892 fungi-Pisp_19787 0.465 fungi-Bden_Batde5_30589 0.89 fungi-Gpro_118574 fungi-Spun_SPPG_02939 Alignment statistics fungi-Aory_CADAORAT00006052 0.986fungi-Anid_7319 0.982fungi-Fgra_CEF84265 0.968 0.812 0.065fungi-Ncra_6406NCU07266 fungi-Tmel_XP_002840026 0.874 fungi-Bade_2079 0.898fungi-Opar_2252 (sequence names) 0.977 0.327 fungi-Scer_5403 0.807 fungi-Ccin_CC1G_04639 0.859 fungi-Spom_2103 0.675 papuso-Nlon_comp14430_c0_seq1_m.20810 fungi-Crev_80093 0.969anim-Mmus_ENSMUSP00000043730 0.873anim-Mmus_ENSMUSP00000139249 0.922anim-Mmus_ENSMUSP00000102114 0.834 0.866anim-Hsap_ENSP00000359127 0.785anim-Ggal_ENSGALP00000008387 0.115 anim-Acar_ENSACAP00000003004 anim-Xtro_ENSXETP00000001225 0.0.86281 anim-Xtro_ENSXETP00000029018 anim-Cmil_SINCAMP00000020967 Number of taxa: 1057 0.729 anim-Lcha_ENSLACP00000007033 anim-Drer_ENSDARP00000022829 0.852 0.993anim-Drer_ENSDARP00000108734 anim-Drer_ENSDARP00000111794 anim-Pema_ENSPMAP00000007982 0.46 anim-Lcom_77976 Haptophyta 0.868 0.991anim-Lcom_84462 0.7830.947 anim-Scil_85097 anim-Dpul_331033 0.914 anim-Tcas_TC014546 0.971 anim-Dmel_FBpp0083673 0.864 anim-Isca_XP_002402579 0.999anim-Cint_ENSCINP00000018685 0.85 anim-Csav_ENSCSAVP00000011057 0.745 anim-Cele_B0491_7_1 0.958 anim-Ocar_g9334_t1 0.8590.952 anim-Smar_012475 0.319 0.998anim-Bflo_126365 0.683 anim-Bflo_286354 0.731 anim-Nvec_XP_001637152 Alignment length: 147 0.445 anim-Acal_524866572 0.948anim-Lgig_213693 Rhodophyta 0.879 anim-Ctel_166705 0anim-Spur_NP_001229622.995 0.876 0.764 anim-Spur_NP_001229591 anim-Skow_XP_002737563 hzoa-Cfra_5559T1 0.997hzoa-Sarc_SARC_03433 0.944 hzoa-Apar_comp64517_c0_seq1m47968 0.931 hzoa-Ihof_2561 0.798 apuso-Pbif_17505 apuso-Pbif_20623 0.989apuso-Pbif_26883 0.403 apuso-Pbif_14171 0.995 hzoa-Sros_PTSG_12498 0.948 hzoa-Mbre_XP_001748419 0.288 glauco-Cpar_23194Contig38384 Chloroplastida hmycota-Falb_H696_03869T0 0.907 anim-Mlei_ML038035a 0.987SARhete-Toce_23128 Parsimony info. sites: 99.30% 0.613 SARhete-Tpse_XP_002286756 0.367 SARhete-Ptri_XP_002178049 0.897 SARhete-Ngad_2678 0.81 SARhete-Esil_CBN79828 SARhete-Aano_F0YE89 0.97 0.997SARhete-Pinf_XP_002901380 0.583 SARhete-Pult_8670 0.702 SARhete-Alai_CCA20050 0.859 SARhete-Aast_16926 0.974SARhete-Spar_SPRG_18083T0 0.592 0.25 SARhete-Sagg_55144 0.966 SARhete-Aker_28817 Rhizaria 0.526 SARhete-Alim_138306 SARalve-Ptet_A0BGB9_A0BGB9 0.999SARalve-Ptet_A0EH83_A0EH83 0.957 SARalve-Tthe_XP_001013692 0.1380.891 0.913SARalve-Imul_286 SARalve-Otri_6131 0.718 fungi-Rall_4799 Missing data: 1.8% 0.973 UP000031776_307 0.876 SARrhiz-Pbra_5138 0.996exca-Gint_1177 0.97 exca-Glam_XP_001708065 exca-Ssal_EST47436 0.872 fungi-Umay_XP_760553 0.836 0.958 fungi-Cneo_XP_571439 SARrhiz-Rfil_3713245_4s1r1 Alveolata hapto-Ehux_236620 0.931 hapto-Ehux_246613 hapto-Chsp_2442 0.936 fungi-Mdap_1999 0.945 0.189 exca-Pesp_828 1SARalve-Pmar_XP_002768966 0SARalve-Pmar_XP_002774748.779 SARalve-Pmar_XP_002772571 1SARalve-Pmar_XP_002769764 0.758SARalve-Pmar_XP_002787448 0.885 anim-Emul_000439900 0.921 anim-Sman_CCD82345 0.88 anim-Bmal_XP_001893629 0.833 0.766 0.811 SARrhiz-Bnat_41308 0.838 SARalve-Gnip_3794 SARalve-Tgon_XP_002367324 Stramenopiles 0.876 0.944 SARalve-Ncan_3127 0.225 0.602 SARalve-Emit_4841 0.834 SARalve-Vbra_93 SARalve-Smin_008542_t1 0.998 SARalve-Smin_008542_t2 0.921 fungi-Aalg_2680 0.927 fungi-Ecun_NP_586449 fungi-Npar_EIJ88061 0.885 SARalve-Tequ_721 0.908 SARalve-Bbig_2962 SARalve-Pfal_Q8IJV5_Q8IJV5 0.72UP000033072_2870 0.833UP000000595_1047 0.861UP000002487_3053 0.913UP000033049_2347 UP000008156_830 Amoebozoa Phylogenetic inference UP000033048_1052 0.983 0.98UP000001979_1347 0.638 UP000000391_1330 0.1810.489 UP000001059_1379 0.428 UP000000459_2255 UP000000663_67 0.943 UP000001882_922 0.764 UP000000674_1086 0.96 UP000005877_1144 0.335 0.928 UP000002408_2042 0.205 UP000010824_556 0.081 UP000000365_382 0.227 UP000002457_1754 0.902 UP000005095_127 0.991 UP000001941_1493 0.906 0.779 0.149 UP000002146_1747 UP000006565_1981 Holozoa 0.835 UP000005741_37 0.861 UP000034723_213 0.981 UP000030624_1125 0.846 UP000002613_783 Maximium likelihood 0.998 0.928 UP000001901_991 0.869 UP000013307_805 UP000002199_1920 0.945 UP000037237_882 0.218 UP000001400_148 0.355 UP000007490_1739 0.883 UP000009231_116 0.481 UP000017867_1698 0.523 0.887 UP000005223_1780 UP000002315_1024 0.958 0.995 UP000001992_775 0.563 UP000014066_1384 Metazoa 0.966 0.79 0.895 UP000008680_215 UP000001931_550 0.96 UP000007478_230 0.406UP000015502_859 0.901UP000001013_1485 0.999 0.993 UP000000810_506 UP000000536_873 0.449UP000001488_738 0.95 UP000001106_427 FastTree default bootstrap 0.27 0.971UP000007722_1054 0.709 UP000000590_1139 1 UP000000805_1236 UP000002061_743 UP000001037_1054 Holomycota 0.994 UP000012076_1134 0.928 UP000012672_1320 UP000014070_1500 0.851UP000032633_3683 0.927UP000005387_912 UP000019772_1707 0.394 0.911UP000006868_2220 0.924embryo-Ppat_XP_001786971 0.943 UP000033163_4142 0.699 0.242 UP000005850_793 UP000037693_2145 1 0.991UP000031563_2361 UP000007279_1250 UP000001195_247 0.922 UP000003081_3967 Jukes-Cantor+CAT 0.79 Others 0.881 UP000002730_136 0.855 UP000013523_3574 UP000002411_2166 0.977 0.96 UP000017590_1406 0.767 UP000002377_802 0.976 UP000005244_205 0.295 SARrhiz-Bnat_142976 0.85 UP000005316_2729 0.942 UP000003671_1469 0.792 UP000011124_1002 UP000008806_316 0.933 0.973 UP000003240_1380 0.72 UP000004324_4148 0.27 0.968 UP000037784_34 0.643 UP000008922_2136 0.656 UP000006554_1277 chloro-Mpus_Micpu187632 UP000006868_2221 apuso-Pbif_30650 UP000004532_3003 0.977 UP000010478_4076 0.134 UP000010471_1646 0.834 UP000010367_3422 0.643 0.744 UP000027395_3033 0.224 UP000006803_2386 0.991UP000033607_4029 0.235 UP000000737_1461 0.838 0.727 UP000001203_183 0.634 UP000010473_1937 0.807 UP000008204_2282 0.843 0.987 UP000010382_2767 UP000002384_4667 0.859 0.984UP000008206_1358 UP000003959_5820 UP000010472_1140 0.985UP000010101_1730 0.844 0.484 UP000010474_5186 0.929 UP000001191_3644 0.731 UP000010378_4156 0.706 UP000019325_1302 0.3270.92 UP000004344_1385 UP000010380_5846 0.1180.616 UP000002511_978 0.695 UP000005766_4155 UP000010384_2592 0.848 UP000002717_84 0.124 UP000001510_466 0.835 UP000010481_130 0.868 0.976 UP000001332_1033 0.075 UP000001405_897 0.871 UP000010480_860 rhodo-Gsul_2655 0.742 UP000001688_882 0.985 UP000010389_2733 0.945chloro-Vcar_XP_002950804 0.719 0.736 chloro-Crei_XP_001692966 chloro-Cvar_EFN58639 0.834 chloro-Mpus_Micpu161739 0.831 0.964 chloro-Otau_XP_003079489 rhodo-Cmer_CMB055C 0.437 0.49 SARhete-Phal_13208 0.821 0.997 SARhete-Pinf_XP_002998208 0.917 0.802 SARhete-Pult_3337 SARalve-Vbra_8441 hzoa-Sros_PTSG_04917 0.288 hzoa-Mbre_XP_001742170 SARhete-Toce_1745 1 SARhete-Tpse_XP_002293639 UP000000323_1379 0.052UP000004200_844 0.824UP000006062_1922 UP000005459_2050 0.668 UP000002964_949 0.887 0.995UP000017935_5450 0.828 UP000034410_295 UP000005167_2486 0.8810.212 UP000015562_1937 UP000031631_2467 UP000000683_363 0.971 0.993UP000001870_2164 0.633UP000009282_3023 0.9830.199UP000011864_1737 UP000001981_3844 0.124 0.799 UP000006334_2977 UP000008888_462 UP000000501_2416 0.801 0.767 0.106UP000034156_1321 0.947UP000001416_158 UP000002718_487 0.7880.719UP000001625_2152 0.404 UP000031637_929 0.693 UP000015559_84 0.792 UP000008291_468 0.973UP000000383_1119 0.173 UP000002742_1834 0.795 0.973 UP000002743_247 UP000002440_2082 0.802UP000004679_1888 0.232UP000003544_403 1 UP000009144_1482 0.881 UP000009145_276 0.985UP000006838_2129 UP000001844_899 0.544 0.972 UP000005744_2647 0.335 UP000031623_594 0.722 anim-Aque_4769 UP000002383_2910 1 UP000010809_2028 0.819UP000019031_2558 0.772UP000029499_3503 0.766UP000004339_3295 0.841UP000008540_2307 UP000031652_5281 0.9290.862UP000000556_1429 0.925UP000029493_2890 0.878 0.5330.706UP000028931_3676 UP000000686_1693 UP000004220_3903 0.8150.196UP000012082_4546 UP000000233_2218 0.015UP000019522_750 0.5490.667UP000009004_464 0.722 UP000002424_2543 SARalve-Vbra_2229 UP000018418_286 0.822UP000017667_420 0.796UP000013121_921 0.7680.278UP000013117_1435 0.758 0.904UP000000430_711 0.987UP000018419_787 0.918 UP000032870_2712 UP000011866_1451 0.336 0.248 0.999UP000002587_248 0.8230.857 UP000009383_848 UP000003395_2776 0.7230.933 UP000004263_2488 UP000004931_1519 UP000033581_1182 0.998UP000005555_1670 0.534 UP000002677_1589 0.715 UP000005317_71 0.77 UP000002793_847 0.597 0.979 UP000004699_440 0.2390.944 UP000009099_2294 0.728 UP000009102_1506 UP000000466_285 0.751UP000000546_1070 0.978 UP000001993_1084 UP000000930_1566 1 UP000002171_2774 0.962 0.856UP000011757_268 UP000037939_3117 0.24UP000005513_1542 0.214 UP000006468_2999 0.615 UP000001176_323 UP000000223_2874 0.977 0.969UP000000948_1200 0.826 UP000004319_22 0.909 UP000005939_379 UP000001399_261 0.757 UP000003704_2192 0.106UP000002759_1011 0.248 0.881 UP000002045_2858 0.261 UP000007966_996 0.926UP000030310_1564 0.716UP000009010_2251 UP000001173_1668 0.963 UP000001806_397 0.97 1 UP000005267_929 0.835 UP000019095_3329 0.282 0.744 UP000005336_269 UP000000607_935 0.822 UP000010320_973 UP000003579_1708 0.895 0.61UP000033511_3021 0.854UP000037848_1255 0.748 0.964UP000033664_564 0.984 UP000030341_2936 UP000004374_2710 UP000000625_1280 0.896UP000003488_559 UP000037393_933 0.312UP000000230_3742 0.590.651UP000008148_4615 0.871UP000017834_3153 0.942UP000009361_1834 0.843 UP000001955_245 0.981 UP000000756_2477 0.871 UP000000756_3928 0.485UP000000233_3410 0.877 0.959UP000009004_2384 0.9 UP000008490_1618 0.93 UP000001225_1567 UP000000547_813 0.151 0.995UP000000998_1496 0.144 UP000007077_3270 UP000033642_1056 0.912 UP000001947_1646 0.969 UP000003395_3235 0 UP000000593_2716 0.924 UP000001231_1548 0.667 UP000002608_648 UP000006859_3401 0.984UP000007966_1536 0.952 UP000001726_3262 0.788 UP000007074_2870 0.902 0.958UP000033495_786 0.985 UP000033765_1588 0.818 0.086 UP000002745_1765 UP000006764_471 0.781 0.91 UP000004169_504 0.891 UP000007058_1183 0.761 UP000018922_3080 0.919 UP000032733_1521 UP000005093_192 0.617 0.945 UP000005634_1384 UP000005380_332 UP000032479_3070 0.981 UP000032749_1938 0.505embryo-Ntab_2493 0.757embryo-Mgut_mgv1a011403m embryo-Acoe_014_00899 0.133 embryo-Bdis_2g44360 0.9520.967embryo-Sbic_03g028760 embryo-Atha_14213 0.835embryo-Atha_30309 0.906 0.874 0.99embryo-Smoe_XP_002976442 0.886embryo-Smoe_XP_002979833 embryo-Mpol_7351 0.2440.897 embryo-Kfla_2734 0.541embryo-Ppat_XP_001762953 chloro-Mpus_Micpu22906 0.793 0.973 chloro-Otau_XP_003082834 1 chloro-Vcar_XP_002952696 0.977 0.908 chloro-Crei_XP_001694702 chloro-Cvar_EFN51184 0.581 hapto-Ehux_213726 0.794 rhodo-Ccri_T00000927001 0.599 rhodo-Cmer_CMV039C 0.5620.58 SARalve-Smin_015591_t1 0.654 0.965 UP000005735_3198 0.832 UP000006633_1910 glauco-Cpar_28081Contig55617 UP000007127_3214 0.929 0.547 0.682 fungi-Spun_SPPG_06177 0.99 papuso-Nlon_comp33263_c0_seq1_m.64844 0.632 UP000037884_4051 UP000002168_4075 0.782UP000006876_4275 0.865hmycota-Nspp_Unigene18922_53916 0.637hmycota-Nspp_Unigene18921_53911 0.737UP000004510_4937 UP000008737_2754 0.8340.969UP000001977_963 0.833UP000026398_2924 0.4190.388UP000001225_754 UP000002676_2657 UP000019805_1706 0.402 0.931UP000033067_2933 0.836 UP000008632_452 0.776 UP000006735_1197 UP000005870_174 0.99 0.598 0.709 UP000004210_2164 0.804 UP000005234_1332 UP000004557_2823 UP000016497_3715 0.954UP000001511_2702 0.75UP000010474_1383 0.435UP000001191_3650 0.436UP000010390_3069 0.889 0.738 UP000004344_806 UP000002483_5271 0.9030.896UP000010378_3966 0.917UP000010381_3069 0 UP000010476_4497 UP000010473_3440 0.788 UP000010389_1596 0.838UP000010382_3956 0.891 glauco-Cpar_18688Contig15671 0.071 UP000010382_1904 0.129UP000008204_2427 0.7160.863 UP000031625_1612 0.995UP000002384_1490 0.8620.477 UP000008206_3533 0.801UP000033607_2108 0.879 UP000008878_3338 0.943 UP000010483_2774 UP000002511_2417 0.475 0.439 UP000001510_4693 UP000034681_217 0.959 UP000000557_1836 UP000000440_2293 0.928 0.906 UP000010379_2215 0.277 UP000001420_77 UP000000758_1301 0.729 UP000033121_2542 0.51 0.999UP000004220_516 0.799 0.399 UP000019522_2858 UP000002287_1543 0.901 UP000034315_574 0.979 0.304 UP000007275_2140 UP000002588_936 0.754UP000000595_2958 0.837UP000033072_378 0.935UP000002487_1535 0.639 UP000033049_2403 UP000000459_2312 0.7740.726UP000010866_937 UP000033048_1035 0.937 0.995UP000001979_1231 UP000001059_1295 0.936 0.106 UP000006622_1136 0.279 UP000000391_298 UP000002146_961 1 UP000005095_185 UP000001903_907 0.858 0.863 0.414UP000010843_3575 0.778 0.928UP000019024_654 0.139UP000001879_1718 0.999 UP000000554_696 0.826 UP000000740_1568 0.926UP000006663_2257 0.941UP000000674_1090 0.985 UP000007807_1983 0.862 0.869 UP000005877_1235 UP000001882_2908 UP000034723_1919 0.93UP000030624_36 0.236 UP000013307_110 0.9970.26 UP000002613_1062 UP000001901_1413 0.473 0.829UP000002574_146 0UP000002574_444.986 0.925 UP000002574_1097 0.171 UP000001366_1633 0.667 UP000000798_188 UP000005981_1841 0.891 0.909UP000002008_2027 0.588 UP000013026_1258 0.671 UP000001916_3082 0.99 UP000000671_7463 UP000007030_2079 0.276 UP000001018_1403 0.966 UP000001974_1173 0.915 UP000001037_1636 0.41 0.203 UP000002593_802 UP000034722_2622 loki2371 UP000002714_116 0.876UP000006431_361 0.948 UP000001118_1777 0.112 0.783 UP000006378_290 0.995 UP000001201_887 UP000000939_169 0.378 UP000016160_446 0.916 UP000031636_755 0.956 UP000032229_1696 0.82 UP000001601_1580 0.645 UP000009186_187 0.734 0.988UP000031466_1521 UP000007590_2983 0.8460.885 UP000004095_6329 0.759 UP000000493_1398 0.869 UP000003919_1089 UP000002875_2855 0.83 papuso-Nlon_comp23210_c0_seq1_m.58445 0.176 UP000002028_1315 1 0.4 UP000011058_4292 0.978 UP000009309_2496 0.884 UP000002011_2046 0.889 0.585 UP000001635_517 UP000002028_549 0.961 UP000011058_2621 0.991 UP000029487_1185 0.858 UP000029507_3375 0.977 UP000007490_2161 0.883 UP000009231_1111 0.429 UP000017867_189 1 UP000005223_161 UP000008680_2019 0.719UP000037693_556 0.924UP000019675_2555 UP000030963_2275 0.722 0.916UP000034887_2681 0.983 UP000003283_3297 0.928 UP000006691_605 0.871 UP000031563_2356 0.856 UP000000742_2366 0.854 UP000034887_1688 0.886 UP000031651_957 0.2880.806 UP000006315_2115 UP000036202_3070 0.964 0.986UP000031982_166 0.443 UP000031563_804 0.864 UP000000935_3478 0.543 UP000009283_3203 1UP000001384_609 0.9610.168 UP000001417_4024 UP000002386_1092 UP000031563_2664 0.804UP000034827_2183 0.885UP000002381_5470 0.743 0.423UP000003891_3530 0.882 UP000030061_277 UP000006868_1955 0.157UP000029487_5156 0.65UP000029519_5112 0.779 0.8980.874UP000019772_1178 0.801UP000029507_2859 0.991 embryo-Ppat_XP_001787048 0.891 0.953 UP000032320_114 0.64 UP000003445_2814 UP000037969_1435 0.894 0.31 UP000004324_1359 0 UP000017966_1598 0.897 UP000006346_268 0.96 UP000035704_2178 0.876 UP000001572_59 UP000001683_365 0.916 UP000002706_1852 0.674 UP000002706_289 0.884 UP000000718_1473 0.982 UP000002521_973 0.906 UP000006875_2571 0.859 UP000002730_1256 UP000028481_1256 0.854 0.933 UP000017925_1293 0.59 UP000018181_452 0.799 UP000018114_776 UP000045545_1172 0.971UP000000590_784 0.986 UP000007722_887 0.747 UP000001106_846 0.807 0.996UP000000805_945 UP000002061_451 UP000017970_1306 0.897 0.65 0.964 UP000018340_1749 0.478 UP000018136_1223 0.77 UP000004756_3134 UP000017904_561 0.505 SARhete-Alim_51245 0.906 SARhete-Sagg_68181 0.164 SARhete-Aker_31469 UP000037784_187 0.749 UP000002514_1925 0.928 1 UP000029986_1486 UP000004508_864 0.77fungi-Mcir_Mucci2_164544 0.808 fungi-Rory_7554 0.995 fungi-Pbla_Phybl2_11683 fungi-Uram_294559 0.885 fungi-Rirr_335035 0.104 0.939 fungi-Mver_05860 hzoa-Apar_comp22317_c0_seq1m33159 0.515 0.811 hzoa-Ihof_5432 0.919 fungi-Ccor_160086 hzoa-Cfra_5164T1 1 hzoa-Sarc_SARC_04137 0.717SARhete-Toce_23396 0.745 0.818 SARhete-Tpse_XP_002289598 0.636 SARhete-Ptri_XP_002180504 SARhete-Aano_F0YPA5 0.888 0.924 SARhete-Esil_CBN77740 0.05 SARrhiz-Bnat_54149 0.907 SARhete-Ngad_9958 0.699 crypto-Gthe_87531 0.04 hzoa-Cfra_4047T1 0.998 hzoa-Sarc_SARC_07205 0.579 hzoa-Cfra_4555T1 hzoa-Awhi_Unigene15887_m9905 0.842 hzoa-Apar_comp6538_c0_seq1m2306 0.969 hzoa-Ihof_8447 0.62 SARhete-Pinf_XP_002896337 1SARhete-Pult_9110 fungi-Aory_CADAORAT00006826 0.953fungi-Anid_3260 0.679 fungi-Fgra_CEF85300 0.645 0.739 0.985fungi-Ncra_550NCU00602 0.918 fungi-Tmel_XP_002839282 0.92 fungi-Opar_4342 0.886 0.843 fungi-Scer_5689 fungi-Bade_2931 0.791 fungi-Spom_1649 0.833 fungi-Mver_09214 0.925 fungi-Rirr_80012 0.918fungi-Mcir_Mucci2_154075 0.792 fungi-Rory_1536 0.994 fungi-Uram_245388 0.983 fungi-Pbla_Phybl2_178202 0.581 0.783 fungi-Umay_XP_760144 0.982 fungi-Cneo_XP_568193 0.694 fungi-Ccin_CC1G_10103 0.874 fungi-Ccor_25552 fungi-Crev_80257 0.791 SARhete-Alim_64489 0.716 SARhete-Sagg_78473 0.858 SARhete-Alim_120677 0.647 SARhete-Aker_23782 0.78 1 SARhete-Aker_35160 0.825 hzoa-Clim_g5610 0.972 hzoa-Clim_g430 0.02 0.808 hzoa-Nk52_10066 0.999 hmycota-Nspp_Unigene9669_29545 fungi-Spun_SPPG_01125 0.843 fungi-Spun_SPPG_01742 fungi-Gpro_33065 hzoa-Mbre_XP_001745780 0.907 anim-Nvec_XP_001617771 hzoa-Sros_PTSG_11107 0.74UP000037991_1883 0.772UP000008043_7237 0.73UP000037687_2754 0.942UP000031501_3 0.868UP000015423_312 0.853 0.949UP000001444_4593 0.988UP000033551_4489 0.818 UP000000377_2516 0.866 UP000032410_1489 UP000008363_1275 0.535 0.204UP000006304_6079 0.99 UP000000757_2368 0.116 UP000006138_6196 0.654 UP000005063_146 0.4680.515 UP000008221_1603 UP000033900_2499 0.963 0.974 UP000002941_1311 0.896 UP000000657_5292 UP000001549_272 0.799 UP000003118_750 UP000027982_1189 0.989 UP000027982_2315 0.75 UP000008960_2282 0.999UP000018350_703

0.7 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgureavailable 20 under aCC-BY-NC 4.0 International license.

fungi-Aory_CADAORAT00006826 100 fungi-Anid_3260 99 fungi-Fgra_CEF85300 100 Taxonomy 99 fungi-Ncra_550NCU00602 fungi-Tmel_XP_002839282 Alignment statistics 99 fungi-Opar_4342 (sequence names) 99 99 97 fungi-Scer_5689 Number of taxa: 80 fungi-Bade_2931 Haptophyta 31 fungi-Spom_1649 fungi-Mver_09214 Alignment length: 226 76 Rhodophyta fungi-Rirr_80012 51 fungi-Rory_1536 Chloroplastida 100 Parsimony info. sites: 89.80% 88 fungi-Mcir_Mucci2_154075 Rhizaria 60 100 fungi-Uram_245388 Missing data: 1.4% fungi-Pbla_Phybl2_178202 fungi-Umay_XP_760144 Alveolata 97 88 100 fungi-Cneo_XP_568193 Stramenopiles 40 fungi-Ccin_CC1G_10103 fungi-Crev_80257 Amoebozoa Phylogenetic inference fungi-Ccor_25552 hzoa-Nk52_10066 69 28 hzoa-Clim_g430 Holozoa Maximium likelihood 81 50 hzoa-Clim_g5610 hmycota-Nspp_Unigene9669_29545 Metazoa 74 1000 UFBoot replicates 45 fungi-Spun_SPPG_01125 fungi-Gpro_33065 Holomycota 55 fungi-Spun_SPPG_01742 Others LG+R5 fungi-Mcir_Mucci2_164544 36 99 100 fungi-Rory_7554 100 fungi-Pbla_Phybl2_11683 98 fungi-Uram_294559 fungi-Mver_05860 98 93 fungi-Rirr_335035 hzoa-Apar_comp22317_c0_seq1m33159 100 84 hzoa-Ihof_5432 46 hzoa-Cfra_5164T1 100 77 hzoa-Sarc_SARC_04137 fungi-Ccor_160086 hzoa-Cfra_4555T1 99 100 hzoa-Sarc_SARC_07205 56 hzoa-Cfra_4047T1 SARhete-Pinf_XP_002896337 100 41 SARhete-Pult_9110 52 hzoa-Awhi_Unigene15887_m9905 SARhete-Toce_23396 100 99 SARhete-Tpse_XP_002289598 93 SARhete-Ptri_XP_002180504 87 SARhete-Aano_F0YPA5 27 SARhete-Ngad_9958 SARhete-Esil_CBN77740 99 57 98 SARrhiz-Bnat_54149 73 crypto-Gthe_87531 hzoa-Apar_comp6538_c0_seq1m2306 100 hzoa-Ihof_8447 SARhete-Alim_64489 57 98 98 SARhete-Sagg_78473 100 SARhete-Alim_120677 SARhete-Aker_23782 100 100 SARhete-Aker_35160 fungi-Spun_SPPG_06177 anim-Nvec_XP_001617771 100 98 hzoa-Mbre_XP_001745780 hzoa-Sros_PTSG_11107 UP000001118_1777 99 UP000006378_290 100 UP000002714_116 99 100 UP000006431_361 56 UP000000939_169 UP000034722_2622 100 37 loki2371 UP000001872_635 93 55 56 UP000002574_444 UP000001366_1633 84 UP000000798_188 UP000005981_1841 61 UP000002008_2027 100 98 UP000013026_1258 100 97 UP000001916_3082 UP000007030_2079 UP000000671_7463

19 27 2

124

Taxonomic group Counts Sampled species counts Holomycota 10 + NIR-NAD(P)H + TPmet Ichthyosporea (Holozoa) 4 + NIR-NAD(P)H - TPmet Choanoﬂagellata (Holozoa) 2 Rhizaria 1 - NIR-NAD(P)H + TPmet Cryptophyta 1 - NIR-NAD(P)H - TPmet Ochrophyta (Stramenopiles) 1 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Supplementary ﬁgure 22

UP000005954_193 95 UP000005964_2056 95 100 UP000004119_628

100 UP000017101_2215 UP000037951_2691 100 UP000036352_1084 100 UP000009381_2124 99 UP000007460_2335 81 UP000001820_2394 78 UP000005759_4959 78 100 UP000001596_4252 UP000005759_3316 UP000029499_1970 97 UP000001192_5842 98 72 UP000001983_1150 97 UP000019095_1277 71 UP000001983_1112 100 UP000003856_2651 97 100 UP000002944_4095 100 58 UP000031843_7189

44 UP000005437_1639 UP000002171_703 100 UP000005634_5090

87 UP000001550_2888 68 UP000002759_2945 98 UP000018548_590 UP000033642_1435 100 UP000011757_1927 100 UP000002171_1770 UP000000270_1149 100 UP000002526_1507 63 99 UP000004510_726 100 UP000005667_4206 99 UP000000374_204 100 UP000003947_5352 100 100 UP000001936_227

53 UP000001820_2300 99 UP000005513_2698 32 UP000003292_3277 UP000001983_1101 100 UP000001983_1128 42 UP000000602_988 100 UP000006034_3224 100 100 UP000006034_495 UP000000602_2733 100 UP000002598_1127 100 UP000006034_1797

78 UP000000556_1002 100 UP000026398_2999 69 86 UP000031521_3404 93 100 UP000000813_2131

77 UP000001868_2804 UP000000361_4778 100 UP000001976_5021 100 100 98 UP000019028_1964

100 UP000006217_2710 UP000033608_1800 UP000033642_1445 UP000003417_3804 96 UP000003417_4290 UP000002515_2974 100 UP000004220_2111 31 UP000006876_1779 32 UP000044377_3213 36 82 UP000007507_458 UP000000374_738 100 UP000000453_4887 75 UP000001994_1414 100 UP000002301_4358 90 88 UP000004510_710 UP000005667_3010 95 UP000032614_7848 57 UP000001035_5492 57 100 UP000008316_5475

89 UP000018548_438

99 76 UP000007296_1208

58 UP000019095_4001 UP000000270_2892 100 UP000003292_1728 100 78 UP000003292_506 UP000036498_699 UP000001983_5371 100 UP000002588_209 99 87 UP000026398_2031 UP000001192_5404 100 72 UP000037884_1539 100 UP000009134_1009 97 UP000001817_626 100 UP000007296_950 100 97 UP000002515_5087 98 UP000004220_3380 UP000005615_2374 100 100 UP000033676_1579 98 UP000006230_5348 94 UP000005667_3619 99 96 100 UP000009319_3457 UP000045063_538 UP000001820_622 99 UP000005759_5108 54 UP000009023_341 100 UP000019443_3973 UP000033434_2908 100 UP000033511_2668 75 UP000033747_2347 100 UP000033449_52 100 100 UP000002943_2037 UP000001424_2719 100 UP000005437_5267 UP000026918_5430 100 UP000013968_1204 100 38 UP000006304_3123 100 UP000009154_2719 100 UP000000640_330 100 UP000002213_5295 100 UP000001318_2457 100 UP000034283_6146 96 100 UP000006728_3015 90 UP000000844_2472 36 98 UP000019225_176 UP000007967_4919 UP000002029_1716 UP000000377_5857 91 37 UP000008703_2545 92 UP000030301_1995 98 92 UP000007947_717 UP000033836_2955 100 100 99 UP000001919_516 92 UP000033572_2451 UP000037432_7371 92 UP000001973_1630 100 33 UP000008914_2486 UP000000851_6842 UP000000428_5928 100 100 UP000037912_9041 100 UP000037687_1468 99 100 UP000004184_3470 UP000037738_87 UP000029482_243 100 100 100 UP000009036_2977 100 UP000031113_1724 100 100 UP000007842_463 UP000033699_3779 16 UP000000343_3896 81 UP000001192_4917 100 46 69 UP000019151_4841 UP000005759_4785 UP000037991_6707 UP000000270_2172 100 UP000037890_3352 100 UP000001624_5592 100 100 UP000001983_4743 UP000001176_3117 UP000037930_2500 100 UP000018851_4057 100 UP000004699_639 96 100 UP000000374_2666 98 100 UP000001306_1173 44 UP000002027_96 59 UP000000442_3857 UP000017640_889 UP000000453_5209 100 UP000002040_2999 100 UP000001624_872 70 100 UP000001600_4713 100 UP000007123_2477 100 43 UP000015480_1968 UP000005143_2844 48 UP000007319_5537 UP000000361_4741 100 UP000037890_759 82 100 UP000037906_2655 100 69 UP000004728_2553 UP000002027_3316 85 UP000004728_2656 97 DM_19360 100 UP000008922_2729 37 UP000002019_994 100 100 UP000034722_1660 CAMPEP_0178999288-Amoebophrya_sp._Strain_Ameob2 UP000034862_641 96 UP000000939_1539 100 UP000006431_1993 94 UP000006378_1635 100 UP000002713_161 100 UP000003180_1268 99 UP000008721_2340 UP000033121_3664 100 UP000002215_2311 100 UP000005438_2925 100 97 UP000007808_1189

95 UP000001822_2290 UP000002028_1311 99 100 100 UP000009309_2499 UP000000493_2010 UP000007364_384 100 100 UP000016160_335 100 100 UP000008634_1764 UP000008461_1880 100 100 UP000001635_3018 100 UP000006073_3847 98 90 UP000004947_1254 UP000001847_1508 100 90 UP000004889_2837 100 UP000004889_763 100 UP000005737_3738 UP000002221_1433 UP000008210_1680 100 UP000008871_1872 98 99 UP000033187_2755 UP000000466_1438 CAMPEP_0168079258-Glenodinium_foliaceum_Strain_CCAP_1116_3 100 CAMPEP_0114611042-Vannella_sp._Strain_DIVA3_517_6_12100 100 CAMPEP_0175941058-Goniomonas_pacifica_Strain_CCMP1869 UP000037660_3098 100 UP000033067_425 93 100 UP000002424_1305

93 UP000002186_2096 UP000000383_2254 100 100 UP000033070_536 100 UP000005267_924 UP000015559_2852 65 UP000001625_2744 100 80 UP000006135_314 UP000009102_1509 99 CAMPEP_0184474976-Thalassiosira_miniscula_Strain_CCMP1093 100 CAMPEP_0184443134-Thalassiosira_miniscula_Strain_CCMP1093 100 94 UP000009145_1036

99 65 UP000000238_1219 UP000009099_2254 UP000003374_295 97 99 UP000005459_4371 99 UP000005167_47 100 UP000031623_921 UP000005744_1339 CAMPEP_0184442034-Thalassiosira_miniscula_Strain_CCMP1093 100 CAMPEP_0183785606-Thalassiosira_miniscula_Strain_CCMP1093 100 CAMPEP_0184440920-Thalassiosira_miniscula_Strain_CCMP1093 100 CAMPEP_0184441150-Thalassiosira_miniscula_Strain_CCMP1093 100 100 UP000037951_2341 UP000000321_1383 100 100 UP000005713_1353 99 UP000032743_243

100 99 UP000033514_54 UP000001959_1305 99 100 UP000006762_1312 UP000017101_3432 99 UP000001492_3389 84 UP000005258_1906 98 99 98 UP000001816_3138 UP000004402_628 100 100 UP000007127_3143 UP000033774_2605 100 UP000006217_1509 99 100 UP000002040_5230 UP000004210_2160 100 UP000018922_886 100 UP000007058_1527 UP000000939_2270 96 UP000009383_23 UP000028868_1603 57 UP000034887_1431 39 UP000036202_3643 48 80 UP000000935_4127

76 UP000013300_3492 UP000031563_1727 76 17 100 UP000001544_2879 UP000000606_3757 100 100 UP000001570_2927 UP000001168_2501 UP000003891_823 91 99 UP000006868_1491 100 100 UP000032633_4540 98 64 100 UP000002510_2525 UP000005387_2664

67 UP000031563_2732 100 UP000034166_1183

93 UP000036202_1881 96 UP000001172_1631 UP000000606_3755 UP000004950_565 88 UP000014104_2546 67 100 100 UP000013858_2361

100 UP000000444_1020

100 UP000029855_1771

35 98 UP000001401_1358 UP000034166_2087 UP000001168_2503 95 100 UP000001544_2897 99 UP000001258_3417 98 27 UP000002368_2870 38 UP000010795_2732 UP000003981_837 100 UP000005387_4052 100 UP000007523_6666 100 99 UP000029431_2376 100 UP000003445_3945 100 100 UP000007523_2148 UP000005850_1027 91 UP000032320_434 100 90 UP000003900_1426

100 UP000005387_867 UP000034883_4898 UP000000671_7460 UP000002043_525 100 UP000002574_1105 100 100 UP000001872_1260

100 UP000000798_187 UP000007382_458 UP000033393_3813 60 60 UP000037746_700 98 UP000019225_3848

95 UP000004926_4866

99 UP000003970_4070

51 UP000002213_4968 UP000007809_2665 52 UP000033603_2569 100 UP000004245_2875 100 UP000037699_2315 100 UP000037773_302 35 92 49 UP000037826_5627 UP000037773_6446 93 UP000037775_6536 100 100 UP000007076_595 93 UP000034283_3360 53 UP000004165_1210 UP000037694_1991 UP000000628_1413 Taxonomy 97 81 UP000004474_350 100 UP000005063_135 100 UP000002255_618 100 UP000009236_575 94 100 100 UP000007962_1296 100 UP000003111_2393 UP000008366_967 84 UP000033425_2529 98 100 UP000033900_3334 100 UP000033448_2418 100 100 UP000008975_2509 UP000000754_1560 26 (euk_db seq. names) 99 UP000006878_2777 UP000000844_4679 100 UP000001908_6071 73 UP000001937_3571 100 UP000001918_858 100 UP000002029_1284 UP000000640_591 100 UP000015971_672 98 100 100 UP000030300_1418 UP000008221_1732 UP000034883_4969 Alignment statistics 100 UP000002139_1311 UP000001116_1315 100 UP000001219_1435 100 91 100 UP000009159_3386

100 UP000006461_3009

100 UP000007947_3281 UP000003448_4271 Haptophyta 100 UP000002139_8309 91 100 100 UP000002257_541

99 UP000027982_1217 UP000005824_5835 100 86 UP000006898_2592 UP000005143_4139 99 UP000005143_4141 Number of taxa: 860 UP000009149_31 UP000000925_491 100 UP000003839_3970 100 UP000001025_6064 58 99 UP000004358_1813 UP000004947_3146 UP000000223_3516 Rhodophyta 100 UP000019522_3658 95 94 UP000002171_2503

87 UP000007077_1732 UP000001113_2756 100 UP000032266_1985 89 UP000002677_573 87 Alignment length: 492 90 UP000005953_744 CAMPEP_0182950320-Acanthoeca_like_sp._Strain_10tr 100 98 UP000011864_3849 98 UP000033581_1768 UP000002168_4078 100 UP000002608_1767 100 Chloroplastida UP000000684_2494 100 98 UP000033633_912 100 UP000000756_3284 UP000032303_4795 52 UP000011866_1395 100 UP000001982_63 100 92 UP000000265_2143 100 UP000001889_1661 99 Parsimony info. sites: 98.20% 99 UP000001702_352 UP000019028_3055 100 69 UP000001726_3264 100 UP000007074_2872 100 UP000007966_1534 Rhizaria 64 UP000006764_1974 100 92 UP000019805_2837 UP000006286_2629 58 UP000032266_5740 96 UP000006286_1441 UP000000430_1578 86 UP000003473_827 UP000004692_118 Missing data: 10.45% 59 100 UP000006282_187 81 60 UP000005090_2720 UP000004263_1026 95 anim-Cgig_10000801 100 100 UP000002713_1031 97 UP000006800_3240 Alveolata 100 UP000007966_466 95 UP000001993_1489

100 UP000033618_296 100 UP000003049_6408 CAMPEP_0174283150-Eutreptiella_gymnastica_like_Strain_CCMP1594 100 100 CAMPEP_0174329750-Eutreptiella_gymnastica_like_Strain_CCMP1594 100 CAMPEP_0113774810-Eutreptiella_gymnastica CAMPEP_0174325250-Eutreptiella_gymnastica_like_Strain_CCMP1594 UP000002505_3129 100 UP000006878_2781 100 98 UP000000628_1080

98 UP000033173_426 99 UP000000322_2747 Stramenopiles 100 UP000000387_1285 UP000033448_2032 73 UP000001919_1416 100 UP000002255_427 61 100 UP000000485_1991 98 UP000009236_573 UP000033956_1616 Phylogenetic inference 100 UP000027986_790 79 UP000008366_3511 96 84 UP000003111_2394 72 UP000007967_81 100 UP000001918_857 91 100 UP000002029_1283 72 UP000030300_4738 Amoebozoa UP000006659_2457 80 UP000011723_1882 100 12 77 UP000035548_452 UP000006138_7782 14 UP000000638_265 100 100 UP000004165_1208

78 UP000009154_2894 79 UP000034330_3145 Maximium likelihood 86 58 UP000002484_716 UP000000844_4678 64 87 UP000008221_1731 UP000000657_5294

90 UP000037743_5714 100 UP000002968_6122 100 Holozoa 96 UP000008703_1474 UP000017765_2272 98 100 UP000006854_2409 92 100 UP000011074_5250 70 UP000001444_7473 79 UP000000851_8013 UP000007575_3095 UP000002139_4225 1000 UFBoot replicates 100 UP000010478_1704 UP000000925_552 52 100 UP000004947_1252 UP000003586_1377 100 U 100 P000003664_166 100 UP000033121_3697 Metazoa UP000009309_2495 99 UP000000493_1397 100 UP000001822_2278 UP000006694_434 99 98 100 UP000016160_731 100 UP000007364_383 UP000008461_6196 LG+F+R10 78 92 UP000001635_3015 93 UP000007808_1183 78 UP000002534_491 UP000001847_1509 100 UP000005737_3733 Holomycota CAMPEP_0118961200-Pyramimonas_obovata_Strain_CCMP722 100 58 CAMPEP_0196581428-Pyramimonas_amylifera_Strain_CCMP720 100 CAMPEP_0182876978-Nephroselmis_pyriformis_Strain_CCMP717 CAMPEP_0183881784-Tetraselmis_striata_Strain_LANL1001 94 UP000003087_3029 100 UP000004358_4856 CAMPEP_0169800140-Symbiodinium_sp._Strain_Mp 28 CAMPEP_0169816492-Symbiodinium_sp._Strain_Mp 28 89CAMPEP_0169804424-Symbiodinium_sp._Strain_Mp CAMPEP_0169693290-Symbiodinium_sp._Strain_Mp 100 CAMPEP_0169885002-Symbiodinium_sp._Strain_Mp 99 100CAMPEP_0169850470-Symbiodinium_sp._Strain_Mp 100CAMPEP_0169739506-Symbiodinium_sp._Strain_Mp Others (including CAMPEP_0169736518-Symbiodinium_sp._Strain_Mp 94 CAMPEP_0169668784-Symbiodinium_sp._Strain_Mp 99 100 CAMPEP_0169905678-Symbiodinium_sp._Strain_Mp CAMPEP_0181523438-Symbiodinium_sp._Strain_CCMP421 100 CAMPEP_0181402576-Symbiodinium_sp._Strain_CCMP421 CAMPEP_0201348404-Symbiodinium_sp._Strain_C15 100 100 100 CAMPEP_0201425594-Symbiodinium_sp._Strain_C15 CAMPEP_0202512174-Symbiodinium_sp._Strain_C1 100CAMPEP_0196987666-Symbiodinium_sp._Strain_D1a 99 MMETSP) 100SARalve-Smin_040143_t1 100 SARalve-Smin_036678_t1

100 CAMPEP_0114639404-Sorites_sp. 100 CAMPEP_0114670234-Sorites_sp. CAMPEP_0115057632-Polarella_glacialis_Strain_CCMP_1383 88 CAMPEP_0115161334-Polarella_glacialis_Strain_CCMP_1383 68 CAMPEP_0115104330-Polarella_glacialis_Strain_CCMP_1383 57 98CAMPEP_0115100130-Polarella_glacialis_Strain_CCMP_1383 100CAMPEP_0115104350-Polarella_glacialis_Strain_CCMP_1383

100 CAMPEP_0198008612-Polarella_glacialis_Strain_CCMP2088 CAMPEP_0176694280-Prorocentrum_minimum_Strain_CCMP2233 100 CAMPEP_0177015240-Prorocentrum_minimum_Strain_CCMP2233 100 CAMPEP_0172778436-Ceratium_fusus_Strain_PA161109 100 CAMPEP_0172930378-Ceratium_fusus_Strain_PA161109 97 CAMPEP_0169193108-Karlodinium_micrum_Strain_CCMP2283 100 87CAMPEP_0169082728-Karlodinium_micrum_Strain_CCMP2283 100 100CAMPEP_0169176266-Karlodinium_micrum_Strain_CCMP2283 CAMPEP_0169299534-Karlodinium_micrum_Strain_CCMP2283 68 CAMPEP_0201215852-Pseudo_nitzschia_fraudulenta_Strain_WWA7 CAMPEP_0181734558-Symbiodinium_sp._Strain_CCMP2430 100 CAMPEP_0196912818-Symbiodinium_sp._Strain_D1a 100 100 CAMPEP_0181478500-Symbiodinium_sp._Strain_CCMP421 CAMPEP_0181535996-Symbiodinium_sp._Strain_CCMP421 100 CAMPEP_0178432838-Amphidinium_massartii_Strain_CS_259 100100 CAMPEP_0178435172-Amphidinium_massartii_Strain_CS_259 97 CAMPEP_0178413294-Amphidinium_massartii_Strain_CS_259 CAMPEP_0178417378-Amphidinium_massartii_Strain_CS_259 100 CAMPEP_0176617714-Amphidinium_carterae_Strain_CCMP1314 100 100CAMPEP_0176549924-Amphidinium_carterae_Strain_CCMP1314 CAMPEP_0196897168-Symbiodinium_sp._Strain_cladeA CAMPEP_0177300602-Scrippsiella_hangoei_like_Strain_SHHI_4 100 CAMPEP_0204090338-Scrippsiella_Hangoei_Strain_SHTV_5 65 CAMPEP_0177313516-Scrippsiella_hangoei_like_Strain_SHHI_4 93 90CAMPEP_0203976634-Scrippsiella_Hangoei_Strain_SHTV_5 100 22CAMPEP_0177161696-Scrippsiella_hangoei_like_Strain_SHHI_4 38CAMPEP_0185012558-Spumella_elongata_Strain_CCAP_955_1 CAMPEP_0177345234-Scrippsiella_hangoei_like_Strain_SHHI_458

87CAMPEP_0183483830-Peridinium_aciculiferum_Strain_PAER_2 CAMPEP_0177440618-Scrippsiella_hangoei_like_Strain_SHHI_4 10073 CAMPEP_0183601180-Peridinium_aciculiferum_Strain_PAER_2 CAMPEP_0177172308-Scrippsiella_hangoei_like_Strain_SHHI_4 CAMPEP_0116540468-Alexandrium_tamarense_Strain_CCMP1771 100 CAMPEP_0116540498-Alexandrium_tamarense_Strain_CCMP1771 78 100 97CAMPEP_0116538472-Alexandrium_tamarense_Strain_CCMP1771

CAMPEP_0116184304-Alexandrium_tamarense_Strain_CCMP1771100

100CAMPEP_0116460024-Alexandrium_tamarense_Strain_CCMP1771

100CAMPEP_0116190734-Alexandrium_tamarense_Strain_CCMP1771 CAMPEP_0116277890-Alexandrium_tamarense_Strain_CCMP1771 CAMPEP_0168043470-Glenodinium_foliaceum_Strain_CCAP_1116_3 84 CAMPEP_0167849014-Glenodinium_foliaceum_Strain_CCAP_1116_3 74 100 96CAMPEP_0168002122-Glenodinium_foliaceum_Strain_CCAP_1116_3

100CAMPEP_0176197834-Kryptoperidinium_foliaceum_Strain_CCMP_1326

100CAMPEP_0167925424-Glenodinium_foliaceum_Strain_CCAP_1116_3 CAMPEP_0176272160-Kryptoperidinium_foliaceum_Strain_CCMP_1326 100 CAMPEP_0176074442-Kryptoperidinium_foliaceum_Strain_CCMP_1326 100 CAMPEP_0176036214-Kryptoperidinium_foliaceum_Strain_CCMP_1326 38 100 CAMPEP_0176107058-Kryptoperidinium_foliaceum_Strain_CCMP_1326 48 CAMPEP_0198614026-Brandtodinium_nutriculum_Strain_RCC3387 CAMPEP_0170208736-Durinskia_baltica_Strain_CSIRO_CS_38 37 CAMPEP_0197703570-Pelagodinium_beii_Strain_RCC1491 CAMPEP_0118276430-Lingulodinium_polyedra_Strain_CCMP_1738 10 7CAMPEP_0117899710-Lingulodinium_polyedra_Strain_CCMP_1738 CAMPEP_0118183134-Lingulodinium_polyedra_Strain_CCMP_17386

100CAMPEP_0118430128-Lingulodinium_polyedra_Strain_CCMP_1738

98 CAMPEP_0118239772-Lingulodinium_polyedra_Strain_CCMP_1738 CAMPEP_0179016074-Pyrodinium_bahamense_Strain_pbaha01 59 100 CAMPEP_0198040780-Heterocapsa_arctica_Strain_CCMP445 100 CAMPEP_0195107716-Heterocapsa_triquestra_Strain_CCMP_448 59 CAMPEP_0168365670-Protoceratium_reticulatum_Strain_CCCM_535___CCMP_1889_

59 CAMPEP_0116401768-Alexandrium_tamarense_Strain_CCMP1771 93 CAMPEP_0116214814-Alexandrium_tamarense_Strain_CCMP1771 100 100 CAMPEP_0116339676-Alexandrium_tamarense_Strain_CCMP1771 CAMPEP_0171213942-Alexandrium_catenella_Strain_OF101 100 100 CAMPEP_0175639406-Alexandrium_monilatum_Strain_CCMP3105 99 CAMPEP_0175464074-Alexandrium_monilatum_Strain_CCMP3105 100 CAMPEP_0175347710-Alexandrium_monilatum_Strain_CCMP3105 CAMPEP_0180605302-Azadinium_spinosum_Strain_3D9 94 100 CAMPEP_0180780922-Azadinium_spinosum_Strain_3D9 88 96 CAMPEP_0197943594-Gonyaulax_spinifera_Strain_CCMP409 CAMPEP_0173637500-Karenia_brevis_Strain_CCMP2229 100 CAMPEP_0178076832-Karenia_brevis_Strain_SP3100 CAMPEP_0174215144-Karenia_brevis_Strain_CCMP2229 CAMPEP_0170586660-Togula_jolla_Strain_CCCM_725 CAMPEP_0201429462-Symbiodinium_sp._Strain_C15 100 CAMPEP_0201352290-Symbiodinium_sp._Strain_C15 100 CAMPEP_0202624282-Symbiodinium_sp._Strain_C1 100 100 100 CAMPEP_0202594598-Symbiodinium_sp._Strain_C1 CAMPEP_0181475984-Symbiodinium_sp._Strain_CCMP421

100 CAMPEP_0181491682-Symbiodinium_sp._Strain_CCMP421 100 100CAMPEP_0181417474-Symbiodinium_sp._Strain_CCMP421 CAMPEP_0181547932-Symbiodinium_sp._Strain_CCMP2430 100 CAMPEP_0169855476-Symbiodinium_sp._Strain_Mp 100 100 CAMPEP_0169647858-Symbiodinium_sp._Strain_Mp CAMPEP_0176576050-Amphidinium_carterae_Strain_CCMP1314 100 100 CAMPEP_0196900918-Symbiodinium_sp._Strain_cladeA 100 CAMPEP_0178428016-Amphidinium_massartii_Strain_CS_259 CAMPEP_0197671854-Pelagodinium_beii_Strain_RCC1491 CAMPEP_0170290506-Durinskia_baltica_Strain_CSIRO_CS_38 48 CAMPEP_0170287118-Durinskia_baltica_Strain_CSIRO_CS_38 100 47 48CAMPEP_0170352856-Durinskia_baltica_Strain_CSIRO_CS_38

100CAMPEP_0170311436-Durinskia_baltica_Strain_CSIRO_CS_38 CAMPEP_0170220250-Durinskia_baltica_Strain_CSIRO_CS_38 100 CAMPEP_0170342970-Durinskia_baltica_Strain_CSIRO_CS_38 100 CAMPEP_0170258072-Durinskia_baltica_Strain_CSIRO_CS_38 CAMPEP_0176335512-Kryptoperidinium_foliaceum_Strain_CCMP_1326 97 CAMPEP_0167846710-Glenodinium_foliaceum_Strain_CCAP_1116_3 60 CAMPEP_0176204050-Kryptoperidinium_foliaceum_Strain_CCMP_1326100 CAMPEP_0176276844-Kryptoperidinium_foliaceum_Strain_CCMP_1326 100 CAMPEP_0176054130-Kryptoperidinium_foliaceum_Strain_CCMP_1326 100 CAMPEP_0176091530-Kryptoperidinium_foliaceum_Strain_CCMP_1326 CAMPEP_0204099036-Scrippsiella_Hangoei_Strain_SHTV_5 100 100 CAMPEP_0203870430-Scrippsiella_Hangoei_Strain_SHTV_5 100 CAMPEP_0177387404-Scrippsiella_hangoei_like_Strain_SHHI_4 100 CAMPEP_0177170328-Scrippsiella_hangoei_like_Strain_SHHI_4 88 CAMPEP_0194792666-Crypthecodinium_cohnii_Strain_Seligo 42 CAMPEP_0194911504-Crypthecodinium_cohnii_Strain_Seligo 100 100 CAMPEP_0194870546-Crypthecodinium_cohnii_Strain_Seligo CAMPEP_0115186864-Scrippsiella_trochoidea_Strain_CCMP3099 38 CAMPEP_0115578258-Scrippsiella_trochoidea_Strain_CCMP3099100 CAMPEP_0115374382-Scrippsiella_trochoidea_Strain_CCMP3099 CAMPEP_0117479846-unnamed CAMPEP_0178310164-Karenia_brevis_Strain_Wilson 100 68 CAMPEP_0178267622-Karenia_brevis_Strain_Wilson CAMPEP_0117330140-Karenia_brevis_Strain_SP1 CAMPEP_0178253382-Karenia_brevis_Strain_Wilson30 33 CAMPEP_0114854448-Karenia_brevis_Strain_Wilson 51 CAMPEP_0178303936-Karenia_brevis_Strain_Wilson 48 CAMPEP_0117126184-Karenia_brevis_Strain_SP1 98 CAMPEP_0117183318-Karenia_brevis_Strain_SP1 75 96 60CAMPEP_0117110030-Karenia_brevis_Strain_SP1 CAMPEP_0114716718-Karenia_brevis_Strain_Wilson 29 CAMPEP_0178140164-Karenia_brevis_Strain_Wilson 31 CAMPEP_0117304950-Karenia_brevis_Strain_SP1

CAMPEP_0117256044-Karenia_brevis_Strain_SP114 CAMPEP_0178009428-Karenia_brevis_Strain_SP3 1187 CAMPEP_0177824266-Karenia_brevis_Strain_SP3 91CAMPEP_0177998170-Karenia_brevis_Strain_SP3 89CAMPEP_0178087680-Karenia_brevis_Strain_Wilson 54CAMPEP_0177865196-Karenia_brevis_Strain_SP3 87CAMPEP_0178119064-Karenia_brevis_Strain_Wilson

98CAMPEP_0177825332-Karenia_brevis_Strain_SP3 CAMPEP_0173756148-Karenia_brevis_Strain_CCMP2229 54 CAMPEP_0114725118-Karenia_brevis_Strain_Wilson CAMPEP_0114842310-Karenia_brevis_Strain_Wilson 71 99 58CAMPEP_0114774788-Karenia_brevis_Strain_Wilson 59 CAMPEP_0178010714-Karenia_brevis_Strain_SP3 100 30CAMPEP_0178252544-Karenia_brevis_Strain_Wilson

CAMPEP_0114854836-Karenia_brevis_Strain_Wilson29

CAMPEP_0114763060-Karenia_brevis_Strain_Wilson58

57CAMPEP_0114716540-Karenia_brevis_Strain_Wilson 100 97CAMPEP_0177824366-Karenia_brevis_Strain_SP3

95CAMPEP_0117161436-Karenia_brevis_Strain_SP1 100 CAMPEP_0177878928-Karenia_brevis_Strain_SP3 CAMPEP_0197964082-Polarella_glacialis_Strain_CCMP2088 88 CAMPEP_0172659144-Ceratium_fusus_Strain_PA161109 CAMPEP_0197621362-Pelagodinium_beii_Strain_RCC1491 CAMPEP_0115619132-Scrippsiella_trochoidea_Strain_CCMP3099 65 95CAMPEP_0115404264-Scrippsiella_trochoidea_Strain_CCMP3099 CAMPEP_0115495098-Scrippsiella_trochoidea_Strain_CCMP309996

67CAMPEP_0115291866-Scrippsiella_trochoidea_Strain_CCMP3099

49CAMPEP_0115281708-Scrippsiella_trochoidea_Strain_CCMP3099 CAMPEP_0115376886-Scrippsiella_trochoidea_Strain_CCMP3099 100 CAMPEP_0115698106-Scrippsiella_trochoidea_Strain_CCMP3099 7896 CAMPEP_0115244936-Scrippsiella_trochoidea_Strain_CCMP3099 CAMPEP_0115491072-Scrippsiella_trochoidea_Strain_CCMP3099100 CAMPEP_0115228724-Scrippsiella_trochoidea_Strain_CCMP3099 CAMPEP_0116469120-Alexandrium_tamarense_Strain_CCMP1771 91 98 CAMPEP_0116179858-Alexandrium_tamarense_Strain_CCMP1771 98 58 70CAMPEP_0116262690-Alexandrium_tamarense_Strain_CCMP1771 CAMPEP_0116174340-Alexandrium_tamarense_Strain_CCMP1771 34 CAMPEP_0116433918-Alexandrium_tamarense_Strain_CCMP1771 10099 CAMPEP_0116350764-Alexandrium_tamarense_Strain_CCMP1771 CAMPEP_0116403396-Alexandrium_tamarense_Strain_CCMP1771 CAMPEP_0181703248-Symbiodinium_sp._Strain_CCMP2430 100 CAMPEP_0196905948-Symbiodinium_sp._Strain_D1a 64 61 61CAMPEP_0181653660-Symbiodinium_sp._Strain_CCMP2430

100CAMPEP_0181589294-Symbiodinium_sp._Strain_CCMP2430

100CAMPEP_0181772786-Symbiodinium_sp._Strain_CCMP2430 CAMPEP_0181426674-Symbiodinium_sp._Strain_CCMP421 100 CAMPEP_0178461980-Amphidinium_massartii_Strain_CS_259 100 52 100 CAMPEP_0178398950-Amphidinium_massartii_Strain_CS_259

69 CAMPEP_0204511116-Alexandrium_margalefi_Strain_AMGDE01CS_322 CAMPEP_0197875924-Gonyaulax_spinifera_Strain_CCMP409 100 CAMPEP_0197943780-Gonyaulax_spinifera_Strain_CCMP409 CAMPEP_0117560170-unnamed 97 CAMPEP_0117499272-unnamed 100 CAMPEP_0175270890-Alexandrium_monilatum_Strain_CCMP3105 97 CAMPEP_0175432622-Alexandrium_monilatum_Strain_CCMP3105 96 CAMPEP_0175430988-Alexandrium_monilatum_Strain_CCMP3105 100 98CAMPEP_0175432830-Alexandrium_monilatum_Strain_CCMP3105 98CAMPEP_0175735496-Alexandrium_monilatum_Strain_CCMP3105 CAMPEP_0175580760-Alexandrium_monilatum_Strain_CCMP3105 81 CAMPEP_0175190572-Alexandrium_monilatum_Strain_CCMP3105 100 81 CAMPEP_0175431840-Alexandrium_monilatum_Strain_CCMP3105 16 76CAMPEP_0175579544-Alexandrium_monilatum_Strain_CCMP3105 CAMPEP_0175199878-Alexandrium_monilatum_Strain_CCMP3105 37 62CAMPEP_0175342502-Alexandrium_monilatum_Strain_CCMP3105 34 95 CAMPEP_0175580306-Alexandrium_monilatum_Strain_CCMP3105 81 CAMPEP_0175579490-Alexandrium_monilatum_Strain_CCMP3105 100 CAMPEP_0175649274-Alexandrium_monilatum_Strain_CCMP3105 CAMPEP_0175484300-Alexandrium_monilatum_Strain_CCMP3105 100 CAMPEP_0171170022-Alexandrium_catenella_Strain_OF101 100 CAMPEP_0171192920-Alexandrium_catenella_Strain_OF101 100 100 CAMPEP_0197817924-Alexandrium_andersonii_Strain_CCMP2222 95 100 CAMPEP_0179034588-Pyrodinium_bahamense_Strain_pbaha01 CAMPEP_0179123158-Pyrodinium_bahamense_Strain_pbaha01 100 100 CAMPEP_0179059624-Pyrodinium_bahamense_Strain_pbaha01 100 CAMPEP_0171071466-Gambierdiscus_australes_Strain_CAWD_149 CAMPEP_0168392596-Protoceratium_reticulatum_Strain_CCCM_535___CCMP_1889_ 100 CAMPEP_0168401802-Protoceratium_reticulatum_Strain_CCCM_535___CCMP_1889_ CAMPEP_0118259492-Lingulodinium_polyedra_Strain_CCMP_1738 98 99CAMPEP_0118338914-Lingulodinium_polyedra_Strain_CCMP_1738 CAMPEP_0117002116-Tiarina_fusus_Strain_LIS 91 CAMPEP_0118423654-Lingulodinium_polyedra_Strain_CCMP_1738 10085 CAMPEP_0118423672-Lingulodinium_polyedra_Strain_CCMP_1738 89 CAMPEP_0117919212-Lingulodinium_polyedra_Strain_CCMP_1738 CAMPEP_0180723070-Azadinium_spinosum_Strain_3D9 100 CAMPEP_0169284050-Karlodinium_micrum_Strain_CCMP2283 100 CAMPEP_0169209486-Karlodinium_micrum_Strain_CCMP2283 100 100 CAMPEP_0169068314-Karlodinium_micrum_Strain_CCMP2283 CAMPEP_0176374032-Strombidinopsis_acuminatum_Strain_SPMC142 77 CAMPEP_0176403488-Strombidinopsis_acuminatum_Strain_SPMC14299 100 100CAMPEP_0176350860-Strombidinopsis_acuminatum_Strain_SPMC142 95 CAMPEP_0195155176-Heterocapsa_triquestra_Strain_CCMP_448

77 CAMPEP_0195058712-Heterocapsa_triquestra_Strain_CCMP_448 CAMPEP_0195157766-Heterocapsa_triquestra_Strain_CCMP_448

56 CAMPEP_0170624058-Togula_jolla_Strain_CCCM_725 100 100CAMPEP_0170618716-Togula_jolla_Strain_CCCM_725 CAMPEP_0170589474-Togula_jolla_Strain_CCCM_725 67 CAMPEP_0198495594-Brandtodinium_nutriculum_Strain_RCC3387 100 CAMPEP_0198531390-Brandtodinium_nutriculum_Strain_RCC3387 CAMPEP_0116912254-Mesodinium_pulex_Strain_SPMC105 78 CAMPEP_0168638916-Heterocapsa_rotundata_Strain_SCCAP_K_0483 30 81 CAMPEP_0168682084-Heterocapsa_rotundata_Strain_SCCAP_K_0483 80 79 CAMPEP_0168679554-Heterocapsa_rotundata_Strain_SCCAP_K_0483

99CAMPEP_0116926910-Mesodinium_pulex_Strain_SPMC105 CAMPEP_0116904760-Mesodinium_pulex_Strain_SPMC105 99100 CAMPEP_0168679388-Heterocapsa_rotundata_Strain_SCCAP_K_0483 99 100CAMPEP_0116950996-Mesodinium_pulex_Strain_SPMC105 100 CAMPEP_0168677746-Heterocapsa_rotundata_Strain_SCCAP_K_0483 82 CAMPEP_0198100438-Heterocapsa_arctica_Strain_CCMP445 CAMPEP_0198099424-Heterocapsa_arctica_Strain_CCMP445 CAMPEP_0195153972-Heterocapsa_triquestra_Strain_CCMP_448 CAMPEP_0184577474-Alveolata_sp._Strain_CCMP3155 CAMPEP_0184569338-Alveolata_sp._Strain_CCMP3155 CAMPEP_0195220328-Skeletonema_dohrnii_Strain_SkelB 100 CAMPEP_0195202586-Skeletonema_dohrnii_Strain_SkelB 100 100CAMPEP_0113383112-Skeletonema_costatum_Strain_1716

100CAMPEP_0201720406-Skeletonema_japonicum_Strain_CCMP2506

100CAMPEP_0201711990-Skeletonema_grethea_Strain_CCMP_1804

64CAMPEP_0183673136-Skeletonema_menzelii_Strain_CCMP793

65 CAMPEP_0172267446-Cyclotella_meneghiniana_Strain_CCMP_338

96 CAMPEP_0172341468-Thalassiosira_sp._Strain_FW CAMPEP_0203359996-Thalassiosira_weissflogii_Strain_CCMP1010 82 CAMPEP_0172311968-Detonula_confervacea_Strain_CCMP_353 82 80 CAMPEP_0181126508-Thalassiosira_sp._Strain_NH16 CAMPEP_0202273392-Thalassiosira_oceanica_Strain_CCMP1005 98 83 100CAMPEP_0202158006-Thalassiosira_oceanica_Strain_CCMP1005 CAMPEP_0202274274-Thalassiosira_oceanica_Strain_CCMP1005

100CAMPEP_0183764322-Thalassiosira_miniscula_Strain_CCMP1093 CAMPEP_0201869896-Thalassiosira_antarctica_Strain_CCMP982 87 97 CAMPEP_0184766786-Thalassiosira_rotula_Strain_CCMP3096 77 CAMPEP_0172574156-Thalassiosira_punctigera_Strain_Tpunct2005C2 CAMPEP_0204761012-Ditylum_brightwellii_Strain_GSO104 84 100CAMPEP_0180959556-Ditylum_brightwellii_Strain_Pop1__SS4_ CAMPEP_0180922936-Ditylum_brightwellii_Strain_Pop1__SS4_ CAMPEP_0181039756-Minutocellus_polymorphus_Strain_NH13 100 100CAMPEP_0181042308-Minutocellus_polymorphus_Strain_NH13 CAMPEP_0185799824-Minutocellus_polymorphus_Strain_RCC2270 100 CAMPEP_0178527834-Extubocellulus_spinifer_Strain_CCMP396 100 CAMPEP_0178505666-Extubocellulus_spinifer_Strain_CCMP396 70 100 100 CAMPEP_0197441104-Triceratium_dubium_Strain_CCMP147 100 76 100 CAMPEP_0113544964-Odontella CAMPEP_0183329258-Odontella_Sinensis_Strain_Grunow_1884 CAMPEP_0197826668-Eucampia_antarctica_Strain_CCMP1452 CAMPEP_0195350528-Chaetoceros_neogracile_Strain_CCMP1317 81 100 84 CAMPEP_0195373410-Chaetoceros_neogracile_Strain_CCMP1317 CAMPEP_0203686590-Chaetoceros_affinis_Strain_CCMP159 82 CAMPEP_0197258902-Chaetoceros_sp._Strain_UNC1202 96 80 100 CAMPEP_0119436456-Chaetoceros_cf._neogracile_Strain_RCC1993 CAMPEP_0194115060-Chaetoceros_debilis_Strain_MM31A_1 100 CAMPEP_0194096896-Chaetoceros_debilis_Strain_MM31A_1 CAMPEP_0178970396-Rhizosolenia_setigera_Strain_CCMP_1694 100 CAMPEP_0178964914-Rhizosolenia_setigera_Strain_CCMP_1694 CAMPEP_0168214822-Pseudo_nitzschia_australis_Strain_10249_10_AB 100 CAMPEP_0168312076-Pseudo_nitzschia_australis_Strain_10249_10_AB 55 CAMPEP_0172367992-Pseudo_nitzschia_pungens_Strain_cf._cingulata 100 CAMPEP_0172407736-Pseudo_nitzschia_pungens_Strain_cf._pungens 56 CAMPEP_0201216598-Pseudo_nitzschia_fraudulenta_Strain_WWA7 100 10056 CAMPEP_0194197638-Thalassiothrix_antarctica_Strain_L6_D1

81 CAMPEP_0197276688-Pseudo_nitzschia_delicatissima_Strain_UNC1205 100 CAMPEP_0197181434-Pseudo_nitzschia_heimii_Strain_UNC1101 CAMPEP_0178745064-Nitzschia_punctata_Strain_CCMP561 100 CAMPEP_0113494840-Nitzschia_sp. 100 CAMPEP_0113482250-Nitzschia_sp. 100 100 CAMPEP_0113452724-Nitzschia_sp. 100 CAMPEP_0113521630-Nitzschia_sp. 100 CAMPEP_0113650420-Cylindrotheca_closterium 100 CAMPEP_0117037602-Tiarina_fusus_Strain_LIS CAMPEP_0119571644-Stauroneis_constricta_Strain_CCMP1120 99 CAMPEP_0172455328-Amphiprora_paludosa_Strain_CCMP125 100 99 CAMPEP_0170685486-Amphora_coffeaeformis_Strain_CCMP127 100 CAMPEP_0168755728-Amphiprora_sp._Strain_CCMP467 19 60 SARhete-Ptri_XP_002180792 CAMPEP_0205121540-Asterionellopsis_glacialis_Strain_CCMP134 100 56 100CAMPEP_0184884660-Asterionellopsis_glacialis CAMPEP_0197145828-Asterionellopsis_glacialis_Strain_CCMP1581 CAMPEP_0198293654-Attheya_septentrionalis_Strain_CCMP2084 56 100 CAMPEP_0202482136-Staurosira_complex_sp._Strain_CCMP2646 CAMPEP_0178911302-Thalassionema_frauenfeldii_Strain_CCMP_1798 100 87 80 70 CAMPEP_0194202386-Thalassionema_nitzschioides_Strain_L26_B CAMPEP_0194071752-Grammatophora_oceanica_Strain_CCMP_410 CAMPEP_0172487702-Coscinodiscus_wailesii_Strain_CCMP2513 100 CAMPEP_0172487902-Coscinodiscus_wailesii_Strain_CCMP2513 CAMPEP_0172426744-Aulacoseira_subarctica_Strain_CCAP_1002_5 100 25 CAMPEP_0195511942-Stephanopyxis_turris_Strain_CCMP_815 CAMPEP_0196803126-Leptocylindrus_danicus_Strain_CCMP1856 100 19 CAMPEP_0116035860-Leptocylindrus_danicus_var._danicus_Strain_B650 CAMPEP_0113311578-Corethron_hystrix_Strain_308 CAMPEP_0184862660-Dactyliosolen_fragilissimus

100 CAMPEP_0195882474-Pelagomonas_calceolata_Strain_CCMP1756 100 100CAMPEP_0195933382-Pelagomonas_calceolata_Strain_CCMP1756 100 CAMPEP_0119232594-Pelagomonas_calceolata_Strain_RCC969 CAMPEP_0195770910-Pelagococcus_subviridis_Strain_CCMP1429 100 CAMPEP_0169058826-Aureococcus_anophagefferens_Strain_CCMP1850 92 54 CAMPEP_0168873608-Aureococcus_anophagefferens_Strain_CCMP1850100 100 CAMPEP_0169041034-Aureococcus_anophagefferens_Strain_CCMP1850 CAMPEP_0118895422-Chrysoreinhardia_sp_Strain_CCMP3193 100 CAMPEP_0198677734-Undescribed_Undescribed_Strain_CCMP2135 CAMPEP_0194693290-Heterosigma_akashiwo_Strain_CCMP2393 100 100 CAMPEP_0179521406-Heterosigma_akashiwo_Strain_CCMP_452 100 CAMPEP_0116734764-Heterosigma_akashiwo_Strain_NB 100 CAMPEP_0116690616-Heterosigma_akashiwo_Strain_NB CAMPEP_0185767086-Dictyocha_speculum_Strain_CCMP1381 97 84 SARhete-Esil_CBJ31380 CAMPEP_0171478654-Vaucheria_litorea_Strain_CCMP2940 CAMPEP_0171490586-Aurantiochytrium_limacinum_Strain_ATCCMYA_1381 100 99 SARhete-Alim_86378 100 SARhete-Aker_101422 SARhete-Sagg_75322 fungi-Anid_7892 100 100 fungi-Aory_CADAORAT00006175 100 fungi-Tmel_XP_002841192

100 fungi-Ncra_4204NCU04720 fungi-Fgra_CEF76735 40 fungi-Bade_2182 100 100 fungi-Opar_3131

32 fungi-Ccin_CC1G_07228 fungi-Uram_177615 100 18 fungi-Mcir_Mucci2_73657 fungi-Rirr_3245 100 fungi-Rirr_250550 100 73 fungi-Spun_SPPG_07925 hzoa-Clim_g4940 95 fungi-Gpro_158697 100 hzoa-Sarc_SARC_08917 100 hzoa-Cfra_4045T1 100 hzoa-Sarc_SARC_08918 100 100 hzoa-Cfra_4044T1 SARhete-Pinf_XP_002900554 100 SARhete-Pult_9450

0.6 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgureavailable 23 under aCC-BY-NC 4.0 International license.

embryo-Mgut_mgv1a005457m 100 100embryo-Mgut_mgv1a004568m 100 embryo-Mgut_mgv1a027122m embryo-Mgut_mgv1a023402m 100 75 embryo-Mgut_mgv1a022931m 75 embryo-Mgut_mgv1a025664m embryo-Ntab_3789 100 92 embryo-Ntab_3446 embryo-Mgut_mgv1a004332m embryo-Atha_30033 89 100 100 embryo-Atha_1756 embryo-Mgut_mgv1a004788m 100 embryo-Atha_18762 96 100 100 embryo-Atha_11637 embryo-Atha_16968 embryo-Acoe_030_00092 100 100 embryo-Acoe_030_00093 embryo-Bdis_3g01277 100 embryo-Bdis_3g01290 100 embryo-Bdis_3g01270 100 100 embryo-Bdis_3g01250 embryo-Sbic_04g001000 41 embryo-Sbic_04g000970 embryo-Mgut_mgv1a019058m 83 100 100 embryo-Mgut_mgv1a004977m 93 embryo-Mgut_mgv1a023971m 83 embryo-Atha_3537 embryo-Sbic_03g032310 100 86 embryo-Bdis_2g47640 embryo-Acoe_002_00061 embryo-Sbic_03g025300 86 100 100 94 embryo-Bdis_2g40740 embryo-Atha_25512 98 embryo-Mgut_mgv1a005911m 100 100 100embryo-Mgut_mgv1a005636m embryo-Mgut_mgv1a006145m embryo-Acoe_002_00060 embryo-Smoe_XP_002966266 98 embryo-Smoe_XP_002993278 embryo-Mpol_14273 98 97 95embryo-Mpol_8180 96embryo-Mpol_15963 100embryo-Mpol_16082 98 embryo-Mpol_14780 97 embryo-Mpol_9278 embryo-Mpol_13200 99 99 embryo-Mpol_10920 embryo-Mpol_11433 100 100 embryo-Mpol_6345 100 100 embryo-Mpol_17009 100 embryo-Mpol_10947 embryo-Mpol_13516 embryo-Ppat_XP_001754130 100 embryo-Ppat_XP_001779265 100 embryo-Ppat_XP_001754049 100 99 96 embryo-Ppat_XP_001768801 embryo-Ppat_XP_001765331 99 embryo-Ppat_XP_001768210 98 100 embryo-Ppat_XP_001768212 embryo-Ppat_XP_001785194 embryo-Kfla_8997 99 embryo-Kfla_5215 81 chloro-Crei_XP_001696788 100 100 chloro-Crei_XP_001696789 95 chloro-Crei_XP_001694496 100 chloro-Vcar_XP_002955238 chloro-Vcar_XP_002955218 100 89 chloro-Vcar_XP_002955217 79 chloro-Vcar_XP_002947869 100 71 100 chloro-Crei_XP_001699931 chloro-Vcar_XP_002947064 chloro-Cvar_EFN52690 98 chloro-Cvar_EFN52689 chloro-Mpus_Micpu49583 100 100 p-NRT2_tblastn_chloro-Otau_NC_014435.1_155021-156448_frame1 hapto-Ehux_62811 100 95 hapto-Ehux_311732 100 hapto-Ehux_440685 97 hapto-Chsp_5066 100 hapto-Ehux_361445 hapto-Ehux_73160 fungi-Anid_3235 100 100 fungi-Aory_CADAORAT00006174 100 fungi-Anid_7526 100 fungi-Tmel_XP_002841190 fungi-Ncra_6351NCU07205 100 fungi-Fgra_CEF72344 100 fungi-Bade_5343 100 100 fungi-Bade_1945 100 100 fungi-Bade_5232 fungi-Opar_3451 fungi-Ccin_CC1G_07229 100 fungi-Umay_XP_759996 100 fungi-Gpro_57051 100 100 fungi-Gpro_131472 100 fungi-Spun_SPPG_01654 fungi-Rirr_30454 100 100 fungi-Rirr_46659 fungi-Mver_08622 100 fungi-Uram_251407 99 SARhete-Hara_4352 100 100 SARhete-Pinf_XP_002903614 100 SARhete-Phal_2142 98 SARhete-Pult_2696 100 100 SARhete-Pult_12610 SARhete-Alai_CCA24412 100 SARhete-Pinf_XP_002900552 88 87 SARhete-Pult_5693 100 SARhete-Pult_12598 SARhete-Pinf_XP_002900550 100 SARhete-Pinf_XP_002900551 SARhete-Ptri_XP_002184871 96 39 SARhete-Ptri_XP_002180934 99 38 SARhete-Tpse_XP_002287398 SARhete-Tpse_XP_002295904 100 38 SARhete-Tpse_XP_002288802 SARhete-Ptri_XP_002177983 88 100 SARhete-Ptri_XP_002178487 96 SARhete-Toce_31243 SARhete-Toce_10904 81 SARhete-Ptri_XP_002185352 82 SARhete-Esil_CBJ31726 98 SARhete-Esil_CBJ31727 100 100 SARhete-Esil_CBJ31725 100 77 77 SARhete-Esil_CBJ31728 SARhete-Aano_F0Y6A2 99 99 SARhete-Aano_F0YL80 SARrhiz-Bnat_55712 100 SARrhiz-Bnat_41977 98 SARrhiz-Bnat_47047 100 100 SARrhiz-Bnat_48035 100 SARrhiz-Bnat_29248 74 SARrhiz-Bnat_47189 SARalve-Vbra_3602 100 100 SARalve-Vbra_21071 100 SARalve-Vbra_691 SARalve-Smin_016992_t1 rhodo-Ccri_T00009493001 100 rhodo-Pyez_15784_g3774 100 Taxonomy rhodo-Gsul_4935 100 97 rhodo-Cmer_CMG018C (sequence names) crypto-Gthe_154872 Alignment statistics glauco-Cpar_675Contig10946 99 99 glauco-Cpar_16401Contig10789 glauco-Cpar_10143Contig53034 Number of taxa: 175 Haptophyta UP000001550_718 100 100 UP000006801_2573 99 UP000007507_2881 Alignment length: 501 Rhodophyta 99 UP000037884_2074 UP000033468_3229 97 Parsimony info. sites: 96.40% Chloroplastida UP000007127_2333 UP000008707_804 98 71 69 UP000000239_2168 Missing data: 8.76 Rhizaria 100 UP000033642_2416 UP000027249_633 99 100 100 UP000018258_1469 Alveolata UP000006242_2222 UP000031623_2421 Phylogenetic inference Stramenopiles UP000002028_1312 100 100 UP000009309_2498 UP000003586_3111 Maximium likelihood Amoebozoa 96 100 100 UP000011058_4290 UP000001822_2291 96 UP000010796_1928 1000 UFBoot replicates Holozoa 100 97 100 UP000001635_3019 UP000006073_2635 LG+F+R8 Metazoa UP000001847_1514 100 61 UP000003087_3028 100 100 UP000010798_5465 Holomycota 100 UP000005943_1948 UP000002221_1430 Others UP000008634_1772 96 UP000008898_1745 100 UP000004690_2917 100 UP000003919_1098

0.4 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgure available24 under aCC-BY-NC 4.0 International license. fungi-Aory_CADAORAT00006175 100 100 fungi-Anid_7892 74 fungi-Tmel_XP_002841192 100 fungi-Ncra_4204NCU04720 96 fungi-Fgra_CEF76735 fungi-Opar_3131 100 100 fungi-Bade_5354 fungi-Ccin_CC1G_07228 92 79 fungi-Umay_XP_759995 fungi-Uram_177615 79 97 fungi-Mcir_Mucci2_73657 fungi-Rirr_3245 55 100 fungi-Rirr_250550 49 fungi-Spun_SPPG_07925 99 fungi-Gpro_158697 SARhete-Pinf_XP_002900554 100 SARhete-Pult_9450 SARhete-Toce_16230 100 100 SARhete-Tpse_XP_002287665 100 100 SARhete-Ptri_XP_002180792 100 SARhete-Aano_F0Y6U7 SARhete-Esil_CBJ31380 92 SARalve-Smin_036678_t1 100 94 SARalve-Smin_040143_t1 78 100 SARalve-Vbra_16973 SARalve-Vbra_1590 UP000004358_4856 100 UP000003087_3029 UP000001635_3015 100 96 UP000010796_2200 98 UP000005438_2929 83 UP000000493_1397 76 UP000002534_491 UP000001847_1509 100 UP000004889_2868 100 UP000001693_3753 85 100 UP000037921_2448 UP000002566_4011 98 UP000000925_552 100 UP000004947_1252 Taxonomy (sequence names) 0.2 Haptophyta Alignment statistics Rhodophyta Number of taxa: 40 Chloroplastida Alignment length: 807 Rhizaria Parsimony info. sites: 78.70% Alveolata Missing data: 1.43% Stramenopiles Amoebozoa Phylogenetic inference Holozoa Maximium likelihood Metazoa 1000 UFBoot replicates Holomycota LG+R5 Others bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Supplementary ﬁgure 25

Alignment statistics

Number of taxa: 418 Alignment length: 260

UP000004732_674_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_Rr_2-17

UP000006871_2109_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ketogulonogenium_vulgarum UP000035287_2256_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Croceicoccus_naphthovorans

UP000009242_1982_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_PP1Y

UP000007515_971_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_AP12

UP000037878_851_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_ST904

UP000004402_4472_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_subarctica UP000005498_1824_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Erythrobacter_sp_SD-21

UP000033874_4820_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_chungbukensis UP000032300_498_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_hengshuiensis UP000033202_1819_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_changbaiensisUP000030907_1549_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingopyxis_fribergensisUP000018851_5974_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sanxanigenens Parsimony info. sites: 96.90% UP000009381_683_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_HTCC2255

UP000005395_2744_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_SKA58 UP000001275_1920_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingobium_sp_SYK-6

UP000033680_2691_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_SRS2

UP000006480_2047_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingobium_sp_AP49 UP000003257_1704_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceanibulbus_indoliflexUP000033997_2895_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_Ag1 UP000002944_2041_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_GAI101 Missing data: 9.99% UP000025047_1186_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Loktanella_hongkongensisUP000015480_804_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Paracoccus_aminophilus UP000004731_1628_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodobacterales_bacterium_HTCC2150UP000000361_4175_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Paracoccus_dentrificansUP000032743_1068_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Paracoccus_sp_361

UP000004318_2382_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pseudooceanicola_batsensis UP000005746_3021_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodobacterales_bacterium_HTCC2083 UP000004119_3123_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_AzwK-3b UP000006833_56_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Dinoroseobacter_shibae UP000003635_255_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceanicola_granulosusUP000033676_4265_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseovarius_sp_217

UP000005713_1091_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sagittula_stellata UP000006230_3489_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Salipiger_bermudensis UP000004701_2070_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_R2A62UP000006765_1974_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceaniovalibus_guishaninsula

UP000037930_1043_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000005759_3113_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Citricella_sp_SE45 UP000003110_1872_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Citreicella_sp_357UP000007753_616_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- Phylogenetic inference UP000036352_106_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ruegeria_algicola UP000037951_2955_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Shimia_sp_SK013UP000028921_528_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000033741_1081_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Loktanella_sp_S4079 UP000004836_821_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_IMCC14465 Maximium likelihood UP000000270_2808_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Azotirhizobium_caulinodansUP000002417_4516_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Xanthobacter_autotrophicusUP000032160_2611_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Phaeomarinobacter_ectocarpi UP000005954_605_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_ISM UP000006633_2070_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Thiobacillus_novellus UP000002686_1550_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Bradyrhizobium_sp_STM3843UP000002930_3176_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodovulum_sp_PH10 1000 UFBoot replicates UP000003148_1114_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_SG-6CUP000002531_2247_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Nitrobacter_winogradskyi UP000001948_151_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodovibrio_parvus UP000008850_1790_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pelagibacterium_halotolerans

UP000033649_1273_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_chinhatensis LG+F+R10 UP000033411_3173_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_epidermidihirudinisUP000033632_1172_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_geojensis Bmal_NP_694908 UP000033519_1977_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_psychrophila

UP000002257_2323_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methylocella_silvestrisUP000033608_2013_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_limiUP000033514_805_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_soli

UP000006309_34042_phylum_-/class_-/sp_uncultured_eubacterium UP000003947_1699_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Microvirga_lotononidisUP000037890_1742_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Bosea_sp_AAP35UP000002526_7_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_-

UP000008207_95_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methylobacterium_nodulans UP000001185_2910_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methylobacterium_sp_4-46 UP000006377_670_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Parvibaculum_lavamentivorans UP000031643_840_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Methyloceanus_cenitepidus UP000018542_418_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hyphomicrobium_nitrativorans UP000033187_3633_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Filomicrobium_sp_YUP000036498_4154_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- Taxonomy

UP000005952_1450_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_X UP000005735_305_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseibium_sp_TrichSKD4UP000008130_1609_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Polymorphum_gilvum Bacteria UP000000494_1499_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000000321_1145_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Aurantimonas_manganoxydansUP000004703_4139_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Stappia_alexandrii UP000004310_37_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Fulvimarina_pelagi Cytophaga-Flexibacter-Bacteroides UP000004291_2990_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hoeflea_phototrophicaUP000038011_1965_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ahrensia_marina UP000003904_1980_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ahrensia_sp_R2A130 Hrob_174267 UP000001820_3473_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_[Mesorhizobium]_sp_BNC1 UP000032025_3797 Planctomycetes UP000045063_4611_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Mesorhizobium_sp_SOD10UP000003250_5653_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Mesorhizobium_alhagi UP000002949_6406_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Mesorhizobium_amorphaeUP000006589_4599_phylum_-/class_-/sp_- Aquiﬁcaeota UP000001565_597UP000033580_1054_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_KarpUP000033616_281_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_DubaiAque_17699 UP000008320_1072_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_ArkansasCrei_XP_001692182 UP000007516_622_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Wolbachia_sp_wOoVcar_XP_002951230 UP000002719_1436_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Brucella_melitensis_bv_Abortus UP000001942_282_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_Miyayama UP000000552_1181_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_loti UP000023755_638_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_no_culture_available [Plastid donors] UP000002480_667_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_Breinl Cyanobacteria UP000007471_348_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000008005_674_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rickettsia_amblyommii UP000001426_3994 UP000002745_2867_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hirschia_balticaIsca_XP_002401674

UP000034392_307_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Altererythrobacter_atlanticus UP000033765_1668_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hyphomonas_sp_c22

UP000033495_2029_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Hyphomonadaceae_bacterium_c29 UP000032611_1743_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Martelella_endophytica UP000004728_1310_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_nitrogenifigens

UP000009081_3079 UP000037880_209_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000037998_1755_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_AAP83 UP000002301_580_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000037906_2412_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_AAP93UP000006011_2501_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceanicaulis_sp_HTCC2633UP000002955_868_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pseudomonas_diminutaUP000028936_440_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rickettsiales_bacterium_Ac37bUP000009286_1329_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Micavibrio_aeruginosavorusUP000001963_187_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Granulobacter_bethesdensis UP000001964_839_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Marinocaulobacter_marisUP000006217_1979_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Acidocella_sp_MX-AZ02 [Mitochondrial donors] UP000009134_3012_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_aromaticivorans Alphaproteobacteria UP000001976_2884_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sinorhizobium_meliloti UP000005667_1225_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Azospirillum_lipoferum UP000037971_460_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_AAP81bUP000002040_1131UP000000245_2579_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000001054_4957_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sinorhizobium_fredii UP000001868_2460_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Phenylobacterium_zucineumUP000006309_87753UP000028946_1037_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Candidatus_Caedibacter_acanthamoebae UP000007319_2928_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Spirillum_lipoferumUP000037884_2960_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_AAP38UP000007127_3869_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_-Acal_168487807Ctel_218805Cele_MTCE_23Opar_4703 UP000034908_1693_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_sp_LC145 UP000033990_1141_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_HIMB114UP000001591_3342_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodospirillum_centenumRhodocista_centenariaCsav_ENSCSAVP00000020160Scer_1388 UP000009181_152_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_marine_bacterium_IMCC9063UP000034491_3076_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Kiloniella_penaeiUP000003292_4616_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Acetobacteraceae_sp_AT-5844Dpul_123676 UP000028181_228_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_galegae UP000002528_1225_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pelagibacter_ubiqueUP000006097_283_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_HIMB59UP000005324_3830_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseomonas_cervicalisUP000028926_224_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Paracaedibacter_acanthamoebaeBade_3824 Betaproteobacteria Pema_ENSPMAP00000011437Spom_4961 UP000001596_762_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_vitis UP000005258_2507_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Tistrella_mobilisLcha_ENSLACP00000021811Hsap_ENSP00000354982Acar_ENSACAP00000021689Mmus_ENSMUSP00000080997Dmel_FBpp0100180Aque_21381Hmag_YP_002221529 UP000007460_1929_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Puniceispirillum_marinumUP000004261_800_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_SAR116_cluster_alpha_proteobacterium_HIMB100Xtro_ENSXETP00000064138Drer_ENSDARP00000087875Ggal_ENSGALP00000034618 UP000000813_1766_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000003417_74_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_BAL199UP000033774_2796_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Elstera_litoralisSkow_YP_337786Tadh_YP_654092Anid_4239 UP000009023_6134_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_sp_CF142 Aque_9374Mbre_NP_696991 Ppal_ABX45141_1Ppal_YP_209604_1 UP000006746_429_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Thalassobaculum_marinaAque_24044Uram_181584Rirr_64177 Gammaproteobacteria UP000006080_5010_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_sp_Pop5 Cmer_CMW011CCang_45014 Smoe_XP_002994289 Esil_CBJ18015Esil_CBH32014Esil_CBH32017 UP000003712_2180_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- Nspp_Unigene17260_50633Ngad_9424Esil_CBH32009Ptri_YP_005090327Phal_14300 UP000001936_4657_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_etli Ntab_1930Atha_1215Ntab_2583Acoe_023_00098Nlon_comp43687_c0_seq1_m.67144 UP000031368_1411_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_gallicum Kfla_705Otau_YP_717297 Others UP000019443_5474_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_favelukesii UP000009319_3164_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhizobium_mesoamericanum UP000001600_1338_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Agrobacterium_sp_13-626 Archaea Euryarchaeotas UP000018922_357_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Magnetospirillum_gryphiswaldense UP000007058_2357_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Magnetospirillum_magneticum Eukaryota

UP000006309_33234 Aque_5423 Taxa with plastid/plastid-related organelles UP000006552_2016_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Aromatoleum_aromaticum 0.8 UP000000383_2438_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Methylotenera_versatilis Other eukaryotes UP000034410_463_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Sedimenticola_thiotauriniUP000002743_2273_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- UP000002383_1321_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Thioalkalivibrio_sulfidophilusUP000002566_2813UP000001436_4615 UP000008210_5855 UP000006838_45_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Nitrosocystis_oceanusUP000006282_2042_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_-UP000031843_2619UP000005808_3484UP000006843_2728 UP000033664_3402 UP000001844_3292_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Nitrosococcus_halophilusUP000002168_3240

UP000000556_5209 UP000006821_2102_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylococcus_capsulatus UP000033684_2521_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylococcaceae_bacterium_Sn10-6

UP000018838_2020_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Legionella_oakridgensisUP000032803_71_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Legionella_hackeliaeUP000044071_1520_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_LegA UP000008490_1050UP000000233_4029 UP000032414_283_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_TATLOCK UP000044377_258_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Brenneria_goodwiniiUP000019028_3523_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_HSUP000001932_1831_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Sodalis_glossinidiusUP000008075_4070_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Xenorhabdus_nematophilus_subsp_nematophilusUP000032721_682_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Xenorhabdus_doucetiaeUP000000756_2837_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000001955_2789_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shimwellia_blattaeUP000008148_2632UP000001889_1592_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Citrobacter_rodentiumUP000001014_4073_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_-UP000001702_2873_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Xanthomonas_uredovorusUP000030307_1117_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_-UP000006631_2560UP000001624_221UP000002759_1432_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Brenneria_sp_EniD312UP000001726_2374_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Erwinia_tasmaniensisUP000006859_939_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_-UP000011001_446_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_-UP000033924_1193_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Erwinia_tracheiphilaUP000019587_2676_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Yersinia_enterocoliticaUP000002334_1881_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_secondary_symbiont_type-T_of_Uroleucon_ambrosiae Hrob_70062 UP000002440_1589_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_strain_KTUP000009073_329_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Tolumonas_auensisUP000030310_2690_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pantoea_sp_PSNIH2 UP000000609_121_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Legionella_pneumophilaUP000032430_3415_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Legionella_fallonii UP000002438_4374_phylum_-/class_-/sp_synthetic_oligonucleotidesUP000025241_4631_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_knackmussiiUP000006755_2419_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Gallaecimonas_xiamenensis UP000002676_546_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- UP000029431_2393_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_larvaeUP000007523_5170_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_mucilaginosusUP000031843_6774UP000005808_2566_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Wautersia_basilensis UP000003445_5752UP000006876_5168_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Alcaligenes_xylosoxydans_xylosoxydansUP000001436_2134_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_solanacearumUP000002566_2480_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_pickettiiUP000008210_5148_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Wautersia_eutropha UP000002770_382_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Legionella_drancourtii UP000037269_1634_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_migulanusUP000007279_1693_phylum_low_GC_Gram+/class_Firmibacteria/sp_-UP000005870_584_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudoxanthomonas_spadixUP000006055_1851_phylum_purple_photosynthetic_bacteria_and_relatives/class_delta_subgroup/sp_Desulfomonile_tiedjei UP000000501_1783_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Nitrosomonas_sp_Is79A3 UP000019675_1694_phylum_low_GC_Gram+/class_Firmibacteria/sp_Lysinibacillus_varians UP000000812_1372_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_PCE-RR UP000037693_162_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_decisifrondisUP000006868_2087 UP000001570_2165 UP000034887_5560 UP000034166_3661_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_campisalis UP000032633_3532_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_beijingensisUP000001225_4303_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Bordetella_petrii UP000003283_4648 UP000030963_4038_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_B14905UP000031982_2665_phylum_low_GC_Gram+/class_Firmibacteria/sp_-UP000004080_2262_phylum_low_GC_Gram+/class_Firmibacteria/sp_Fictibacillus_macauensisUP000026398_1577_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Bordetella_hinzii UP000006654_2969_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_medusa UP000000935_3927UP000017805_1129 UP000004417_2024_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_SG-1UP000034029_2555_phylum_low_GC_Gram+/class_Firmibacteria/sp_Salinicoccus_haloduransUP000028868_2303_phylum_low_GC_Gram+/class_Firmibacteria/sp_-UP000027985_1801_phylum_low_GC_Gram+/class_Firmibacteria/sp_Virgibacillus_sp_SK37UP000030061_5470_phylum_low_GC_Gram+/class_Firmibacteria/sp_-UP000002510_582_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sp_JDR-2

UP000036202_1400 UP000037908_275_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_CHD6a UP000001963_1154UP000001977_1096_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Bordetella_avium UP000042335_1576_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_B-jeddUP000001570_2307UP000001355_3385_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_nhkUP000006843_2040_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Vibrio_marinopraesens UP000029855_1575_phylum_low_GC_Gram+/class_Firmibacteria/sp_Listeria_newyorkensisUP000034272_247_phylum_-/class_-/sp_Parcubacteria_group_bacterium_GW2011_GWA1_47_8UP000032634_4380_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderia_uboniaeUP000002350_1782_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_violaceaUP000002168_4295_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_woodyi UP000036353_662_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_smithii UP000000605_3328_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Pseudomonas_pseudomalleiUP000004703_5310 UP000031496_2202_phylum_low_GC_Gram+/class_Firmibacteria/sp_Planococcus_sp_PAMC21323 UP000004950_2007_phylum_low_GC_Gram+/class_Firmibacteria/sp_Listeria_fleischmanniiUP000002287_1909_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_-UP000001436_3164 UP000003900_4960_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_dendritiformisUP000032320_594_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sp_IHBB_10380UP000034887_1176_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_SA1-12UP000004319_2906_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000037693_2500UP000031651_2556_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_sp_OxB-1 UP000000529_819_phylum_Chlamydiae/class_Chlamydiia/sp_Protochlamydia_amoebophila UP000029519_159_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sp_FSL_H7-0737UP000029507_1645_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_stelliferUP000019772_822_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sabinaeUP000000817_2710_phylum_low_GC_Gram+/class_Firmibacteria/sp_- UP000002381_1728UP000034827_3505_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sp_DMB20 UP000005316_763_phylum_low_GC_Gram+/class_Firmibacteria/sp_Sporosarcina_newyorkensisUP000003891_2961_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_lactisUP000039860_990_phylum_Chlamydiae/class_Chlamydiia/sp_Rubidus_massiliensisTadh_XP_002119092 UP000034315_3995_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- UP000006691_2472_phylum_low_GC_Gram+/class_Firmibacteria/sp_- UP000019095_1309_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Tetrathiobacter_mimigardefordensisUP000035352_442_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_[Polyangium]_brachysporum UP000000366_3099_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Methylibium_petroleiphilum UP000001693_3680_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Leptothrix_cholodniiUP000018548_1798_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- UP000004949_1697_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Gluconobacter_morbiferUP000000496_2369_phylum_Chlamydiae/class_Chlamydiia/sp_strain_Z UP000008944_1058_phylum_low_GC_Gram+/class_Firmibacteria/sp_Staphylococcus_pettenkoferi

UP000006801_8_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_- UP000030061_1284 UP000037960_1279_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_beta_proteobacterium_AAP99 UP000004674_568_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Burkholderiales_bacterium_JOSHI_001UP000006697_2708_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herminiimonas_arsenicoxydansUP000008392_3516_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Collimonas_group_C UP000000531_1836

UP000007296_4066_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbaspirillum_sp_CF444UP000002429_5499_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_-

UP000007507_2248_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbaspirillum_sp_YR522 UP000008207_651 UP000000329_1523_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Herbispirillum_seropedicense UP000031138_2379_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000007437_579_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Paraburkholderia_rhizoxinicaUP000003511_641_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Paraburkholderia_kirkiiUP000004277_2090_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Ralstonia_sp_PBA

UP000001171_2481_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_-

UP000010382_1427_phylum_cyanophytes/class_-/sp_Pleurocapsa_minor

Pfal_Q7HP05_Q7HP05 UP000007077_1158_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_- UP000033633_2404_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_halotoleransUP000002186_3462_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Thauera_sp_MZ1T UP000032303_4178_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Photobacterium_gaetbulicola UP000008840_935_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_strain_MGB_[[Stenotrophomonas_africana]]UP000008186_387_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Shewanella_oneidensis UP000001890_1149_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Xanthomonas_albilineans_var_paspali

UP000005953_1528_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Reinekia_blandensis

UP000008229_1536_phylum_actinobacteria/class_Thermoleophilia/sp_Conexibacter_woesei UP000001172_2386_phylum_low_GC_Gram+/class_Firmibacteria/sp_-

UP000002386_2060_phylum_low_GC_Gram+/class_Firmibacteria/sp_- UP000011864_5542_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Paraglaciecola_psychrophila

Emul_900000000 UP000000557_2234_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_violaceus UP000000466_2179_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Simiduia_agarivoransUP000035081_2622_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinobacter_salarius UP000033747_1906_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Marinomonas_sp_S3726UP000000229_145_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_mendocina

UP000004485_193_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_gamma_proteobacterium_IMCC2047UP000004339_4444_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_sp_M47T1 UP000019031_812_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_papaveris

UP000033581_2037_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Gammaproteobacteria_bacterium_c0UP000004679_1344_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylophaga_thiooxydansUP000019522_23_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_stutzeri UP000002424_873_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Azotobacter_vinelandii

UP000000742_621_phylum_low_GC_Gram+/class_Firmibacteria/sp_Bacillus_flavothermus

UP000006898_64_phylum_candidate_phylum_NC10/class_-/sp_Methylomirabilis_oxyfera UP000031652_1162_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Pseudomonas_sp_StFLB209

UP000005555_2152_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_marine_gamma_proteobacterium_HTCC2207

UP000002209_759_phylum_candidate_division_BD/class_Gemmatimonadetes/sp_Gemmimonas_aurantiaca

UP000000276_811_phylum_actinobacteria/class_high_GC_Gram+/sp_Mycobacterium_tuberculosis-ovis

UP000007882_1396_phylum_actinobacteria/class_high_GC_Gram+/sp_Actinoplanes_missouriensis UP000023703_420_phylum_actinobacteria/class_high_GC_Gram+/sp_Corynebacterium_glycinophilum UP000003981_1301_phylum_low_GC_Gram+/class_Firmibacteria/sp_Paenibacillus_sp_oral_taxon_786

UP000019151_1995_phylum_candidate_division_BD/class_Gemmatimonadetes/sp_Gemmatirosa_kalamazoonesis

UP000008922_1235_phylum_green_nonsulfur_bacteria/class_Anaerolineae/sp_Anaerolinea_thermophila

Sman_CCD63157

UP000031637_2553_phylum_purple_photosynthetic_bacteria_and_relatives/class_beta_subgroup/sp_Sulfuritalea_hydrogenivorans

UP000004664_1245_phylum_purple_photosynthetic_bacteria_and_relatives/class_gamma_subgroup/sp_Methylobacter_tundripaludum bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Supplementary ﬁgure 26

Alignment statistics

UP000001938_1372_phylum_cyanophytes/class_-/sp_Cyanobacteria_sp_Yellowstone_B-Prime

UP000017396_1995_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_kilaueensis Number of taxa: 473 UP000000557_2470_phylum_cyanophytes/class_Gloeobacteria/sp_Gloeobacter_violaceus

UP000003950_2331_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7001

UP000010383_3691_phylum_cyanophytes/class_-/sp_Geitlerinema_sp_PCC_7407 Alignment length: 754 UP000001332_4424_phylum_cyanophytes/class_-/sp_Oscillatoriales_cyanobacterium_JSC-12UP000001115_416_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RCC307 UP000000788_1599_phylum_cyanophytes/class_-/sp_Prochlorococcus_maritima UP000010385_260_phylum_cyanophytes/class_-/sp_Synechococcus_sp_Rippka_B2UP000002935_470_phylum_cyanophytes/class_-/sp_Synechococcus_sp_SYNUP000010472_298_phylum_cyanophytes/class_-/sp_Crinalium_epipsammum UP000002511_4040_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7425UP000004972_3_phylum_cyanophytes/class_-/sp_Synechococcus_sp_RS9916

UP000010388_1881_phylum_cyanophytes/class_-/sp_Cyanobium_gracile

UP000010367_1377_phylum_cyanophytes/class_-/sp_Phormidium_acuminatum Parsimony info. sites: 85.90% UP000010366_4835_phylum_cyanophytes/class_-/sp_Sphaerogonium_minutum UP000010384_3737_phylum_cyanophytes/class_-/sp_Croococcidiopsis_thermalis UP000010476_2518_phylum_cyanophytes/class_-/sp_Chroococcus_sp_Cey_unUP000010478_544_phylum_cyanophytes/class_-/sp_Oscillatoria_nigroviridis

UP000010471_5972_phylum_cyanophytes/class_-/sp_Oscillatoria_sp_McUP000003959_4957_phylum_cyanophytes/class_-/sp_Moorea_producta

UP000010481_2605_phylum_cyanophytes/class_-/sp_Aphanothece_halophytica_'Solar_Lake'UP000010477_1633_phylum_cyanophytes/class_-/sp_Calothrix_parietina Missing data: 50.68% UP000010475_917_phylum_cyanophytes/class_-/sp_Cylindrospermum_stagnaleUP000010390_3250_phylum_cyanophytes/class_-/sp_Calothrix_sp_PCC7507UP000010381_4350_phylum_cyanophytes/class_-/sp_Nostoc_sp_PCC_7107UP000010474_892_phylum_cyanophytes/class_-/sp_Anabaena_cylindrica UP000005766_1139_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC7335UP000001511_3412_phylum_cyanophytes/class_-/sp_Trichormus_azollae UP000003835_7061_phylum_cyanophytes/class_-/sp_Microcoleus_chthonoplastesUP000019325_2819_phylum_cyanophytes/class_-/sp_Nodularia_spumigenaUP000001191_4334_phylum_cyanophytes/class_-/sp_Nostoc_punctiforme

Mgut_mgv11b019259m

UP000010380_2314_phylum_cyanophytes/class_-/sp_Rivularia_sp_LIPUP000000268_2673_phylum_cyanophytes/class_-/sp_- UP000008878_3373_phylum_cyanophytes/class_-/sp_Trichodesmium_erythraeumUP000001420_1414_phylum_cyanophytes/class_-/sp_- UP000000737_1080_phylum_cyanophytes/class_-/sp_Lyngbya_sp_PCC_8106 UP000010379_3397_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_6312UP000010386_2418_phylum_cyanophytes/class_-/sp_Pseudanabaena_sp_PCC7367 UP000001510_2253_phylum_cyanophytes/class_-/sp_Microcystis_aeruginosa UP000031625_1319_phylum_cyanophytes/class_-/sp_cyanobacterium_endosymbiont_of_Epithemia_turgidaUP000033607_1748_phylum_cyanophytes/class_-/sp_Lyngbya_robusta UP000004532_658_phylum_cyanophytes/class_-/sp_- UP000004344_2301_phylum_cyanophytes/class_-/sp_- UP000002384_3725_phylum_cyanophytes/class_-/sp_Synechococcus_sp_PCC_7424UP000008206_5294_phylum_cyanophytes/class_-/sp_Cyanothece_sp_PCC_7822UP000010378_3757_phylum_cyanophytes/class_-/sp_- UP000034681_3344_phylum_cyanophytes/class_-/sp_Prochlorothrix_hollandicaUP000010473_2691_phylum_cyanophytes/class_-/sp_Stanieria_cyanosphaera UP000010480_2953_phylum_cyanophytes/class_-/sp_Cyanobacterium_aponinumUP000010382_1687_phylum_cyanophytes/class_-/sp_Pleurocapsa_minor Phylogenetic inference UP000010389_2963_phylum_cyanophytes/class_-/sp_Leptolyngbya_sp_PCC_7376UP000010483_1031_phylum_cyanophytes/class_-/sp_Cyanobacterium_stanieriUP000010101_2180_phylum_cyanophytes/class_-/sp_- Otau_XP_003080335 UP000027395_1143_phylum_cyanophytes/class_-/sp_- UP000001405_895_phylum_cyanophytes/class_-/sp_cyanobacterium_UCYN-AUP000006803_4828_phylum_cyanophytes/class_-/sp_- UP000003922_3560_phylum_cyanophytes/class_-/sp_Erythrosphaera_marinaUP000001425_3029_phylum_cyanophytes/class_-/sp_-Cvar_gi331268127refYP_004347776 Maximium likelihood UP000000440_25_phylum_cyanophytes/class_-/sp_-

UP000001688_2967_phylum_cyanophytes/class_-/sp_- Mgut_mgv1a026855m UP000008204_2477_phylum_cyanophytes/class_-/sp_- UP000001026_1630UP000001423_1395 UP000005593_2097 1000 UFBoot replicates UP000002535_438UP000001422_608UP000002717_2397Vcar_XP_002959793 UP000001566_512

Otau_YP_717215

Sbic_03g017580 Crei_NP_958365

UP000002483_27Gsul_4735 Bdis_2g41285 Bdis_1g05757 UP000002586_347_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Magnetococcus_marinus

Smoe_XP_002993891

LG+R10 Atha_3725 Ntab_2104 UP000033220_3116_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodospirillum_photometricumUP000001203_2867 Ntab_626 UP000033468_2521_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodospirillaceae_bacterium_c57 UP000005258_4328_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Tistrella_mobilis

Toce_368

Ptri_YP_874393 UP000001929_3447_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Spirillum_rubrumToce_29370 Cmer_CMV096C Toce_27958Aano_C6KIR1 Tpse_XP_002297530 UP000032733_3026_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Magnetospira_sp_QH-2Ppat_XP_001757311 Esil_CAT18825

Ppat_NP_904171 Kfla_1386

UP000007058_469_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Magnetospirillum_magneticumNgad_2331 UP000004169_2194_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodospirillum_molischianum UP000028926_1354_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Paracaedibacter_acanthamoebae UP000028946_887_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Candidatus_Caedibacter_acanthamoebae UP000002222_49 UP000007127_3112_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_-

UP000003180_356_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfurovum_sp_AR UP000002714_185_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Thiomicrospira_denitrificansUP000006431_482_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfurimonas_gotlandica UP000004261_1383_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_SAR116_cluster_alpha_proteobacterium_HIMB100 UP000003082_530_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Wolinella_rectaUP000006380_353_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Wolinella_curvaUP000008633_1538_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Salsamentum_denitrificans UP000002407_1169_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Candidatus_Campylobacter_hominisUP000005709_241_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Campylobacter_gracilisUP000006378_207_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfurovum_sp_NBC37-1 UP000002495_887_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Heliobacterium_hepaticusUP000029857_566_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_bilisUP000003107_1469_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Campylobacter_showae UP000010821_200_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_heilmanniiUP000007803_696_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfurimonas_autotrophica UP000006746_1396_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Thalassobaculum_marina UP000004083_370UP000008387_1017_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_strain_StorkisUP000006036_1774_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_westmeadii UP000033774_1627_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Elstera_litoralis UP000007934_1390_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_felisUP000000760_1365_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Vibrio_fetus UP000000429_1209_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_pyloriUP000001522_393_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_mustelaeUP000000939_87_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_strain_CI UP000007460_571_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Puniceispirillum_marinum UP000004660_984_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Helicobacter_winghamensisUP000000799_443_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_-UP000008721_531_phylum_purple_photosynthetic_bacteria_and_relatives/class_not_Epsilobacteria/sp_Sulfuricurvum_kujiense 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Atha_26514 UP000006762_3469_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Celeribacter_baekdonensis UP000004318_4042_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pseudooceanicola_batsensis UP000007307_778_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_no_culture_available UP000006309_37905_phylum_-/class_-/sp_uncultured_eubacteriumUP000005746_630_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodobacterales_bacterium_HTCC2083 UP000004119_128_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_AzwK-3bUP000004731_2948_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodobacterales_bacterium_HTCC2150UP000036352_2943_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Ruegeria_algicola UP000000361_2232_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Paracoccus_dentrificansUP000003257_1531_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceanibulbus_indoliflexUP000028921_140_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_-UP000033676_4078_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseovarius_sp_217UP000005713_147_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sagittula_stellataUP000001023_4109_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Silicibacter_pomeroyiUP000018780_3389_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Leisingera_methylohalidivorans UP000033741_1478_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Loktanella_sp_S4079UP000015480_1681_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Paracoccus_aminophilusUP000006230_2953_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Salipiger_bermudensisUP000002914_3723_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Phaeobacter_inhibens UP000031521_201_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Celeribacter_indicus UP000005135_3111_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodobacterales_bacterium_KLH11UP000005964_4086_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_SK209-2-6UP000005943_1349_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_MED193 UP000029829_1838_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_-UP000002944_2438_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_sp_GAI101UP000005954_516_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_ISMUP000005759_547_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Citricella_sp_SE45UP000005093_1166_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Silicibacter_lacuscaerulensis UP000001943_954_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_Webster UP000003635_3685_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Oceanicola_granulosusUP000037951_227_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Shimia_sp_SK013 Crei_NP_042564 UP000002703_1208_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodosphaera_minorUP000007029_3448_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Roseobacter_denitrificansUP000003110_3574_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Citreicella_sp_357 UP000002480_45_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_BreinlCang_45012 UP000002361_1226_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rhodopseudomonas_capsulatus Ppal_YP_209572_1Ppal_ABX45156_1Crev_94902Rirr_38717 Anid_5860Uram_286222Uram_160564 UP000008005_774_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Rickettsia_amblyommiiUP000033616_207_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_DubaiUram_156986Bade_2900Scer_6445 Nspp_Unigene14689_44196Spom_4434 Opar_1852Mbre_NP_696989 UP000033769_1520_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_Karp Tequ_1153 Scer_2428Tadh_YP_654083 UP000033454_556_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_KarpPfal_Q7HP03_Q7HP03 UP000033364_1843_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_KarpUP000008850_2695 UP000033580_1586_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_strain_KarpTmel_XP_002838537Nvec_XP_001627028Nvec_XP_001637942 Hrob_65375 Tgon_XP_002372123 Hmag_YP_002221537Adig_20651v102257Hrob_79072 Tgon_XP_002369065 Skow_YP_337791 UP000011816_128 Scer_2005 Acal_45655858 UP000001989_1381 Bade_4612 Dmel_FBpp0100186

Hrob_66922 UP000032025_2288 Scer_1330 Cele_MTCE_21 Bade_3839 Ggal_ENSGALP00000034623Xtro_ENSXETP00000064144 Hsap_ENSP00000354554 Lcha_ENSLACP00000021817 Pema_ENSPMAP00000011430Drer_ENSDARP00000087881Acar_ENSACAP00000021695 Csav_ENSCSAVP00000020157Bmal_NP_694907 Mmus_ENSMUSP00000081003 Sman_CCD63158 Taxonomy Emul_900000150Emul_900000100 Tthe_NP_149395 Bacteria Cytophaga-Flexibacter-Bacteroides Planctomycetes Aquiﬁcaeota Cyanobacteria [Plastid donors] Alphaproteobacteria [Mitochondrial donors] Betaproteobacteria Gammaproteobacteria Others

UP000037880_41_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_-

UP000037930_3288_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- UP000033514_2710_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_soli

UP000033608_2751_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_limi Archaea UP000007753_2844_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_-

UP000033649_522_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_chinhatensisUP000033632_3515_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_geojensisUP000033201_1857_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_- Euryarchaeotas UP000033519_666_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_psychrophila UP000008850_262_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Pelagibacterium_halotolerans

UP000033411_1172_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Devosia_epidermidihirudinisUP000008808_283_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Erythrobacter_litoralis

Eukaryota UP000005498_1185_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Erythrobacter_sp_SD-21 UP000034392_1366_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Altererythrobacter_atlanticus UP000035287_1408_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Croceicoccus_naphthovoransUP000037996_2370_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Porphyrobacter_sp_AAP60

UP000033680_1456_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_SRS2UP000033200_1372_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_taxi UP000007515_4345_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_AP12UP000037998_647_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_AAP83

UP000001275_2309_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingobium_sp_SYK-6 UP000037906_412_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_sp_AAP93

Taxa with plastid/plastid-related organelles UP000033997_729_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_Ag1 UP000006480_1782_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingobium_sp_AP49 UP000009134_3251_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_aromaticivorans UP000005395_3335_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sp_SKA58

UP000033202_2955_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_changbaiensisUP000006578_1838_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingopyxis_alaskensis

UP000030907_1059_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingopyxis_fribergensis

UP000018851_1530_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_sanxanigenens Other eukaryotes UP000004728_1101_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Novosphingobium_nitrogenifigens UP000033874_3734_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_Sphingomonas_chungbukensis

UP000037971_863_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_AAP81b

UP000009381_1086_phylum_purple_photosynthetic_bacteria_and_relatives/class_alpha_subgroup/sp_alpha_proteobacterium_HTCC2255 0.8 bioRxiv preprint doi: https://doi.org/10.1101/454272; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Supplementary ﬁgureavailable 27 under aCC-BY-NC 4.0 International license.

UP000013117_1435 100 UP000013121_921 100 UP000017667_420 86 100 UP000018418_286 85 UP000004263_2488 UP000004931_1519 93 UP000035013_1535 64 UP000000546_1070 100 UP000001993_1084 100 UP000000930_1566 100 UP000002171_2774 100 UP000011757_268 UP000002332_721 88 UP000029499_3503 30 84 UP000005437_4608 9196 UP000017175_4887 100 UP000019031_2558 93 UP000031652_5281 98 UP000029493_2890 UP000000686_1693 100 UP000009004_464 85 57 100UP000019522_750 UP000005555_1670 UP000002793_847 64 UP000005615_1013 99 UP000004699_440 66 91 96 UP000019205_58 32 UP000000466_285 UP000000998_1496 100 UP000007077_3270 47 UP000002587_248 100UP000009383_848 100 UP000009099_2294 96 UP000009102_1506 84 UP000004692_1980 36 UP000005317_71 100 UP000000233_3410 100 UP000001225_1567 95 UP000000547_813 81 UP000033642_1056 UP000000998_3037 UP000004200_844 100 UP000006062_1922 100 UP000005459_2050 100 UP000002964_949 100 UP000017935_5450 100 UP000031631_2467 8 76 UP000034410_295 99 UP000005167_2486 55 UP000002383_2910 91 UP000010809_2028 62 anim-Aque_4769 61 UP000005744_2647 43 98 UP000031623_594 89 SARalve-Smin_015591_t1 UP000003544_403 100 UP000004679_1888 100 UP000009144_1482 98 100 UP000009145_276 20 UP000001844_899 UP000000501_2416 71 100 UP000034156_1321 100 UP000002718_487 69 74 UP000001625_2152 57 UP000031637_929 73 UP000015559_84 UP000000383_1119 100 UP000002742_1834 100 UP000002743_247 UP000000683_363 26 100 UP000001870_2164 100 UP000009282_3023 51 UP000006327_1375 100UP000011864_1737 100 55 UP000001981_3844 96 UP000006334_2977 UP000008888_462 93 rhodo-Cmer_CMV039C 92 UP000037939_3117 32 SARalve-Vbra_2229 100 UP000005513_1542 100 UP000006468_2999 100 UP000001176_323 UP000000223_2874 19 100 UP000000948_1200 100 100 UP000004319_22 100 UP000005939_379 98 UP000003704_2192 UP000001399_261 UP000006764_471 UP000001173_1668 100 UP000001806_397 87 UP000006497_928 100 UP000030310_1564 98 UP000002759_1011 100 UP000007966_996 100 100 UP000009010_2251 100 UP000002045_2858 99 UP000002514_3926 87 UP000004105_1502 87 UP000005336_269 95 UP000000607_935 98 UP000005267_929 100UP000019095_3329 94 UP000003579_1708 100 UP000033511_3021 100 UP000037848_1255 83 100 UP000033664_564 100 UP000030341_2936 81 UP000004374_2710 UP000000684_854 100 UP000002608_648 81 UP000001231_1548 81 100 UP000034071_1816 UP000010320_973 100UP000001889_1821 85 UP000008148_4615 100 UP000000230_3742 94 UP000037393_933 100 UP000000260_2273 100 100UP000009361_1834 100 UP000001955_245 100 UP000030901_30 100 UP000000756_2477 UP000000756_3928 100 hmycota-Nspp_Unigene18922_53916 100 UP000004510_4937 100 hmycota-Nspp_Unigene18921_53911 88 UP000002676_2657 97 UP000008632_452 100 UP000033067_2933 76 96 100 UP000006735_1197 100 UP000016497_3715 UP000005234_1332 100 UP000006859_3401 100 UP000007966_1536 100 UP000007074_2870 88 UP000001726_3262 100 UP000030071_930 91 UP000032749_1938 97 100 UP000001947_1646 100 UP000003395_3235 92 UP000000593_2716 77 UP000032479_3070 100 UP000033495_786 100 UP000033765_1588 97 UP000002745_1765 UP000005380_332 embryo-Mgut_mgv1a011403m 100 embryo-Ntab_2493 98 embryo-Acoe_014_00899 100 embryo-Atha_14213 99 100 embryo-Atha_30309 embryo-Bdis_2g44360 100 embryo-Sbic_03g028760 100 100embryo-Smoe_XP_002976442 100 embryo-Smoe_XP_002979833 100 embryo-Mpol_7351 94 99 embryo-Ppat_XP_001762953 embryo-Kfla_2734 32 chloro-Mpus_Micpu22906 90 100 chloro-Otau_XP_003082834 chloro-Crei_XP_001694702 78 100 chloro-Vcar_XP_002952696 95 chloro-Cvar_EFN51184 100 rhodo-Ccri_T00000927001 hapto-Ehux_213726 100UP000000233_2333 100 UP000019522_2858 Taxonomy 78 100 UP000005729_1906 98 UP000004220_516 86 100 UP000007275_2140 30 UP000034315_574 57 100 UP000002287_1543 100 UP000002588_936 papuso-Nlon_comp33263_c0_seq1_m.64844 (sequence names) 100UP000037884_4051 UP000004169_504 100 UP000007058_1183 UP000033121_2542 83 100 UP000001332_1580 100 UP000002384_1637 100 glauco-Cpar_18688Contig15671 100 UP000000557_1836 97 UP000000440_2293 Haptophyta UP000001420_77 83 UP000033741_1676 100 UP000038011_1445 UP000000758_1301 UP000000459_2312 76 UP000010866_937 12 UP000033048_1035 12 UP000001059_1295 Rhodophyta 60 UP000006622_1136 100 98 UP000002487_1535 11 98 UP000033072_378 100 100 UP000000595_2958 UP000033049_2403 72 UP000000391_298 Chloroplastida UP000002146_961 100 UP000005095_185 100 UP000005741_680 97UP000001903_907 88 97 UP000010843_3575 100 UP000001879_1718 Rhizaria 44 UP000010878_3404 100 UP000000740_1568 44 UP000006663_2257 59 100 UP000015381_2856 UP000000554_696 68 100 UP000004595_2931 89 UP000000390_743 Alveolata 100 UP000030624_36 100 UP000034723_1919 99 UP000002613_1062 UP000013307_110 88 UP000001901_970 100 UP000013307_944 71 46 UP000001901_1413 Stramenopiles UP000001882_2908 UP000034722_2622 100loki2371 69 UP000001444_4593 74 UP000015423_312 73 UP000031501_3 83UP000037687_2754 UP000007170_217 Amoebozoa 81 UP000008043_7237 100UP000037432_8329 85 UP000000428_1095 10094 UP000003022_4047 72 UP000037991_1883 100 UP000037912_7927 100 UP000033551_4489 Holozoa UP000000377_2516 UP000002204_4066 99 UP000032410_1489 99 UP000018781_44 100 99 UP000006304_6079 98 100UP000008190_2332 100 UP000008363_1275 Metazoa 100 UP000000757_2368 100 100 UP000003970_7474 100 UP000006138_6196 99 UP000006728_5467 100 UP000007809_493 UP000002029_8196 Holomycota 98 UP000003118_750 100 UP000005063_4012 UP000000849_1037 99 98 UP000008221_1603 100 UP000002941_1311 98 99 UP000004281_2147 Others 98 UP000033900_2499 UP000005063_146 82 UP000001549_272 glauco-Cpar_28081Contig55617 55 100 UP000000674_1090 100 UP000007807_1983 63 UP000005877_1235 UP000004508_864 57 UP000027982_1189 100 UP000027982_2315 chloro-Mpus_Micpu161739 100 chloro-Otau_XP_003079489 100 chloro-Cvar_EFN58639 99 chloro-Crei_XP_001692966 100 chloro-Vcar_XP_002950804 69 100 SARhete-Phal_13208 69 100 SARhete-Pinf_XP_002998208 100 SARhete-Pult_3337 71 SARalve-Vbra_8441 rhodo-Gsul_2655 70 hzoa-Sros_PTSG_04917 100 98 hzoa-Mbre_XP_001742170 SARhete-Toce_1745 100 SARhete-Tpse_XP_002293639 84 90 rhodo-Cmer_CMB055C SARhete-Alim_51245 100 SARhete-Sagg_68181 96 63 100 SARhete-Aker_31469 52 71 UP000007490_2161 86 UP000008680_2019 98 UP000017867_189 81 UP000005223_161 apuso-Pbif_30650 90 100 UP000000590_784 89 UP000007722_887 89 UP000000805_945 UP000002061_451 UP000002706_1852 100 UP000004095_6329 98 UP000007590_2983 87 UP000007435_236 UP000000493_1398 89 UP000004690_1861 100 UP000032229_1696 61 100 UP000009186_187 98 UP000001635_517 100 UP000003919_1089 papuso-Nlon_comp23210_c0_seq1_m.58445 81 97 UP000011058_2621 UP000008960_2282 100 UP000018350_703 76 UP000004756_3134 100 UP000017941_2269 100 UP000018246_1945 99 UP000008953_3457 100 UP000017970_1306 99 UP000018136_1223 UP000000370_2405 59 100 UP000003803_777 82 99 UP000005435_606 99 UP000017998_1568 100 100 UP000018114_776 UP000009222_2093 89 100 UP000002521_973 63 100 UP000004505_1242 100 UP000006875_2571 81 98 UP000000845_105 UP000002730_1256 UP000017925_1293 100 UP000018181_452 UP000003244_1406 100 UP000003283_3297 100 UP000034887_2681 100 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0.7