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Supporting Information: Figure S1abcd. Supplementary phylogenetic trees. Values at nodes represent support from ML bootstrap pseudoreplicates. (a) Multi-gene ML phylogeny of Tremblaya within Betaproteobacteria inferred from 49 concatenated protein sequences. (b) Zoomed-in Tremblaya ML phylogeny inferred from the 16S-23S rRNA alignment. (c) Multi-gene mealybug ML phylogeny inferred from the 419 concatenated CEGMA protein sequences. (d) ML phylogeny of gammaproteobacterial symbionts inferred from the 16S-23S rRNA alignment. Clade labels A-G were adopted from Thao et al. 2002. Figure S2ab. Schematic diagrams of insect scaffolds containing HGTs involved in amino acid and B-vitamin metabolism. Insect exons (predicted by GeneMark ES) are color-coded as green rectangles and when in close proximity to HGTs, annotated by their putative functions. Genes of bacterial origin are highlighted in yellow. (a) Genome localization of bioABD, ribAD, lysA, dapF, and tms HGTs confirming that they are present on insect scaffolds. Only the longest scaffold for each HGT is shown as the scaffolds from different mealybug species share gene order. (b) Alignments of M. hirsutus, P. marginatus and F. virgata scaffolds showing cysK acquisition after divergence of Maconellicoccus clade and cysK duplication in F. virgata (also present in P. citri and P. longispinus), and riboflavin transporter duplication in P. marginatus. Figure S3a-u. Phylogenetic trees for individual HGTs. Values at nodes represent support from ML bootstrap pseudoreplicates. Extremely short inner branches were extended by dashed lines for better legibility. Table S1ab. Supplementary tables with Tremblaya gene information. (a) Gene order, functional categories from Clusters of Orthologous groups (COG), Enzyme Commission numbers (E.C.), protein products, and gene abbreviations for all Tremblaya genomes. Tremblaya phenacola PAVE inversion is designated by light yellow color, pseudogenes are in red, non-coding RNAs in magenta (tRNAs are not shown), and hypothetical proteins in blue. (b) Raw data to reproduce Figure 3. There are two copies of leuA in TPTPER and two copies of aroDQ in DEMHIR. Only glyS is found in TPPAVE, not glyQ. Legend: 0=missing gene, 1=found on the endosymbiont genome, 2=pseudogene, 3=HGT found on the insect genome, 4=insect gene. Table S2. Extended assembly metrics for draft mealybug genomes. All values were calculated without endosymbiont and low-coverage contamination contigs. BUSCOs Arthropoda assessments for Acyrthosiphon pisum genome assembly as a reference: C:72% [D:6.1%], F:15%, M:12%. Table S3. Supplementary table listing insect scaffolds containing horizontally transferred genes. Longest scaffolds for each of the HGT candidates are in bold. Table S4. Overview of evidence that the HTGs are encoded on the insect genomes. Related to Figures 4 and S3. Table S5. Tremblaya primers. These primers were used for duplicated ribosomal RNA operons and one more region breaking assemblies of the five Tremblaya princeps genomes. Supplementary Figures 1b) 85 Tremblaya princeps from Paracoccus nothofagicola 94 Tremblaya princeps from Sarococcus comis Tremblaya princeps Tremblaya princeps from Cyphonococcus alpinus 57 93 Tremblaya princeps from Antonina crawii 76 Tremblaya princeps from Antonina pretiosa Tremblaya princeps from Trionymus perrisii 63 Tremblaya princeps from Amonostherium lichtensioides 74 62 Tremblaya princeps from Crisicoccus azaleae 82 51 Tremblaya princeps fromMelanococcus albizziae Tremblaya princeps from Australicoccus grevilleae 100 TPTPER Tremblaya princeps from Nipaecoccus exocarpi Tremblaya princeps from Paracoccus marginatus 0.95 TPPMAR 97 1a) Tremblaya princeps from Planococcus citri 100 50 0.99 TPPLON 99 Alcaligenaceae (10) Tremblaya princeps from Planococcus ficus 1 0.75 Tremblaya princeps from Planococcus kraunhiae Tremblaya princeps TPPCIT Tremblaya princeps from Erium globosum 0.73 73 Tremblaya princeps from Pseudococcus calceolariae 1 55 Tremblaya princeps from Dysmicoccus boninsis TPFVIR Tremblaya princeps from Pseudococcus longispinus (Gatehouse et al., 2012) 100 Tremblaya princeps from Pseudococcus longispinus Tremblaya princeps from Dysmicoccus neobrevipes 1 100 TPMHIR 99 Tremblaya princeps from Dysmicoccus neobrevipes Tremblaya princeps from Dysmicoccus brevipes 100 Tremblaya princeps from Pseudococcus viburni (Thao et al., 2002) TPPAVE 0.91 Tremblaya princeps from Pseudococcus viburni (Gatehouse et al., 2012) 100 51 Tremblaya princeps from Pseudococcus longispinus (Thao et al., 2002) Tremblaya phenacola 98 Tremblaya princeps from Pseudococcus longispinus (Munson et al., 1992) Tremblaya princeps from Pseudococcus comstocki 0.92 Tremblaya princeps from Vryburgia brevicruris 99 Tremblaya princeps from Vryburgia amaryllidis 56 Tremblaya princeps from Ferrisia sp. 100 Tremblaya princeps from Ferrisia malvastra Tremblaya princeps from Ferrisia virgata 100 Tremblaya princeps from Anisococcus ephedrae 0.89 100 Tremblaya princeps from Maconellicoccus hirsutus Tremblaya princeps from Maconellicoccus hirsutus Lautropia mirabilis ATCC_51599 (Burkholderiaceae) 100 Tremblaya princeps from Maconellicoccus australiensis Tremblaya phenacola from Phenacoccus solani clone PG24 0.72 99 Tremblaya phenacola from Phenacoccus solani clone PG67 Tremblaya phenacola Sutterella wadsworthensis 3_1_45B (Sutterellaceae) 96 Tremblaya phenacola from Phenacoccus solenopsis clone ctn01 Tremblaya phenacola from Phenacoccus manihoti clone NH112 100 1 100 Tremblaya phenacola from Phenacoccus peruvianus Tremblaya phenacola from Phenacoccus madeirensis clone PG21 1 Parasutterella excrementihominis YIT_11859 (Sutterellaceae) 100 Tremblaya phenacola from Phenacoccus madeirensis 50 Tremblaya phenacola from Heterococcus nudus clone NH20 100 Tremblaya phenacola from Phenacoccus sp. clone NH18 56 Tremblaya phenacola from Phenacoccus avenae 1 1 Thiomonas (2) Tremblaya phenacola from Heliococcus clemente clone PG74 100 Tremblaya phenacola from Phenacoccus aceris clone NH19 1 Tremblaya phenacola from Phenacoccus azaleae 96 50 Tremblaya phenacola from Mirococcus sp. clone NH16 1 Comamonadaceae (23) Tremblaya phenacola from Oxyacanthus sp. clone NH12 0.71 80 Tremblaya phenacola from Peliococcus turanicus clone NH17 Oxalobacteraceae (6) 0.05 1 0.98 1 Burkholderiaceae (83) 1 Limnobacter (Burkholderiaceae) Rhodocyclaceae (6) 1d) Endosymbiont of Crisicoccus azaleae clade C 1 52 99 Endosymbiont of Antonina pretiosa Gallionellaceae (2) 1 Endosymbiont of Antonina crawii 1 51 Nitrosomonadaceae (5) Endosymbiont of Australicoccus grevilleae 1 98 1 81 Endosymbiont of Melanococcus albizziae Hydrogenophilaceae (1) Endosymbiont of Amonostherium lichtensioides Methylophilaceae (7) 1 Hoaglandella endobia TPER Neisseriaceae (54) 97 Moranella endobia PCIT 1 clade E 99 Endosymbiont of Planococcus ficus 0.6 Endosymbiont of Planococcus kraunhiae Mikella endobia PMAR clade G Endosymbiont of Cyphonococcus_alpinus clade D 1c) 99 Endosymbiont of Paracoccus nothofagicola Gullanella endobia FVIR clade B Trionymus perrisii 100 Endosymbiont of Dysmicoccus brevipes 100 79 Endosymbiont of Dysmicoccus neobrevipes 97 Paracoccus marginatus Endosymbiont of Pseudococcus comstocki 97 Endosymbiont of Erium globosum 100 cladeA Pseudococcus longispinus Endosymbiont of Vryburgia amaryllidis Endosymbiont of Ferrisia virgata clone P28 (Rosenblueth et al. 2012) 100 Doolittlea endobia MHIR clade F Planococcus citri Endosymbiont 1 of Pseudococcus longispinus 100 Endosymbiont of Pseudococcus longispinus (Lopez-Madrigal et al. 2014) Ferrisia virgata Endosymbiont 2 of Pseudococcus longispinus 99 Endosymbiont of Pseudococcus longispinus clone P10 (Rosenblueth et al. 2012) Maconellicoccus hirsutus Endosymbiont of Pseudococcus longispinus (Duron et al. 2008) 0.02 0.1 2a) tyrosine-protein phosphatase lysA (FVIR) non-receptor type 4 WD repeat-containing protein 24-like hormone receptor aromatic-L-amino-acid (secretin family) (tyrosine) decarboxylase lysA Hypoxia-inducible bioA (MHIR) DNA polymerase delta Nudix hydrolase-like factor 1-alpha bioB (MHIR) bioD (MHIR) tms (MHIR) tmstms tms ribosomal protein L23A catalytic subunit protein inhibitor hypothetical protein uncharacterized protein, cathepsin B-like bioA cytokine receptor-like bioB bioD 85/88 kDa calcium- Eukaryotic initiation splicing factor 3B subunit 2 like protein hypothetical protein protein ariadne-2 hypothetical protein independent phospholipase A2 factor 4A-III like ribD (FVIR) facilitated trehalose ribA (MHIR) ribD dapF (MHIR) transporter Tret1-like ribA dapF protein singed hypothetical protein probable peroxisomal acyl- coenzyme A oxidase 1 SET and MYND domain- ribonuclease Z, mitochondrial isoform hypothetical AAA-ATPase protein like protein containing protein 2b) histone H2B-like riboflavin transporter histone H3-like histone H2A-like cAMP-dependent protein kinase R2 histone H4-like histone H1-like Maconellicoccus hirsutus 34,593 bp cysK 1 Paracoccus marginatus 27,801 bp histone H3-like histone H2A-like cysK 2 cysK 1 riboflavin transporter cAMP-dependent protein kinase R2 histone H2B-like Ferrisia virgata 43,541 bp 3a) bioA (Alphaproteobacteria or Bacteroidetes) 1 gi 916972895 ref WP 051579607.1 adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Neorickettsia helminthoeca] 1 gi 506296687 ref WP 015816462.1 adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Neorickettsia risticii] gi 499771270 ref WP 011452004.1 adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA [Neorickettsia sennetsu] 0.54 gi 503716903 ref WP 013950979.1 adenosylmethionine--8-amino-7-oxononanoate
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