Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press What Was the Real Contribution of Endosymbionts to the Eukaryotic Nucleus? Insights from Photosynthetic Eukaryotes David Moreira and Philippe Deschamps Unite´ d’Ecologie, Syste´matique et Evolution, UMR CNRS 8079, Universite´ Paris-Sud, 91405 Orsay Cedex, France Correspondence: [email protected] Eukaryotic genomes are composed of genes of different evolutionary origins. This is espe- cially true in the case of photosynthetic eukaryotes, which, in addition to typical eukaryotic genes and genes of mitochondrial origin, also contain genes coming from the primary plastids and, in the case of secondary photosynthetic eukaryotes, many genes provided by the nuclei of red or green algal endosymbionts. Phylogenomic analyses have been applied to detect those genes and, in some cases, have led to proposing the existence of cryptic, no longer visible endosymbionts. However, detecting them is a very difficult task because, most often, those genes were acquired a long time ago and their phylogenetic signal has been heavily erased. We revisit here two examples, the putative cryptic endosymbiosis of green algae in diatoms and chromerids and of Chlamydiae in the first photosynthetic eukaryotes. We show that the evidence sustaining them has been largely overestimated, and we insist on the necessity of careful, accurate phylogenetic analyses to obtain reliable results. oday it is widely accepted that photosynthe- filose amoeba that hosts a cyanobacterium with Tsis originated in eukaryotes by the endosym- a reduced genome that has been described as biosis of a cyanobacterium within a heterotro- “a plastid in the making” (Marin et al. 2005; phic eukaryotic host. This occurred in a line- Keeling and Archibald 2008; Nowack et al. age that subsequently diversified to give rise to 2008). Primary endosymbioses resulted in the the three contemporary groups of primary pho- establishment of plastids with two membranes. tosynthetic eukaryotes: Viridiplantae (includ- However, a vast variety of eukaryotes possess ing green algae and land plants), Rhodophyta plastids with three or more membranes. They and Glaucophyta, grouped collectively within a derive from the endosymbioses of primary pho- unique eukaryotic superphylum called Archae- tosynthetic eukaryotes within other eukaryotic plastida (Adl et al. 2005) or Plantae (Cavalier- cells (Delwiche 1999; Keeling 2013). Such sec- Smith 1982). Recently, a second case of primary ondary endosymbioses have spread photosyn- endosymbioses has been unveiled thanks to the thesis across the eukaryotic tree, either by the characterization of Paulinella chromatophora,a endosymbiosis of red or of green algae. Whereas Editors: Patrick J. Keeling and Eugene V. Koonin Additional Perspectives on The Origin and Evolution of Eukaryotes available at www.cshperspectives.org. Copyright # 2014 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a016014 Cite this article as Cold Spring Harb Perspect Biol 2014;6:a016014 1 Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press D. Moreira and P. Deschamps it is almost certain that secondary endosymbi- origin in their nuclear genomes. This has been oses of green algae occurred twice (in euglenids shown for a variety of nonphotosynthetic eu- and chlorarachniophytes), secondary red algal karyotes, such as, for example, apicomplexan plastids are found in a variety of alveolates, stra- parasites (Fast et al. 2001; Roos et al. 2002; Wil- menopiles, cryptophytes, and haptophytes, and liams and Keeling 2003; Huang et al. 2004), the number of red algal endosymbioses at the perkinsids (Stelter et al. 2007; Matsuzaki et al. origin of these groups has been matter of intense 2008; Ferna´ndez Robledo et al. 2011) or non- debate (Baurain et al. 2010; Keeling 2010, 2013; photosynthetic dinoflagellates (Sanchez-Puerta Burki et al. 2012b). Moreover, the existence of et al. 2007; Slamovits and Keeling 2008), and tertiary endosymbioses (namely, the symbiosis green algae (de Koning and Keeling 2004). Al- of a secondary photosynthetic eukaryote within though much more controversial, potential another eukaryotic cell) and of plastid replace- EGTs have also been used to propose a photo- ments makes the picture of plastid evolution synthetic ancestry for ciliates (Reyes-Prieto et al. in eukaryotes even more complex. Dinoflagel- 2008) or that algae with secondary plastids of lates, some of which have replaced their ances- red algal origin, such as diatoms and chromer- tral red algal plastids by green algae, diatoms, ids, may have contained green algal endosymbi- haptophytes, or cryptophytes, are paradigmatic onts in their past (Moustafa et al. 2009; Woehle examples of such complex situations (Keeling et al. 2011). Likewise, several dozens of potential 2013). EGTs have been detected in algae and plants The evolution of plastids has been studied that appear to have been acquired from Chla- using genes from the plastid genome as well as mydiae, a group of parasitic bacteria (Huang typical eukaryotic nuclear genes, which allow and Gogarten 2007; Becker et al. 2008; Moustafa inferring the phylogenies of both the plastids et al. 2008), which led to proposing that cryp- and their hosts. The use of those markers has tic chlamydial endosymbionts may have helped led to interesting discoveries, such as the mono- to establish the first plastids, in particular, by phyly of the Archaeplastida (Moreira et al. 2000; providing essential functions for plastid activity Rodrı´guez-Ezpeleta et al. 2005) or the difficul- (Greub and Raoult 2003; Ball et al. 2013; Baum ties in reconciling the plastid and host histories 2013). in eukaryotes with red algal plastids (Baurain Werevise here some of these cases of cryptic et al. 2010; Burki et al. 2012b). However, a third endosymbiosis, with special attention on the class of genes can also provide useful comple- difficulties in accurately detecting EGT and the mentary information: the genes of plastid ori- importance of proper phylogenetic analysis and gin retrieved within the nuclear genome of the of an adequate taxonomic sampling to achieve host. In fact, contemporary plastids have small that task. genomes, which is due to the fact that most of the original cyanobacterial symbiont genes CRYPTIC GREEN ALGAL ENDOSYMBIOSES were lost or transferred to the host nucleus (by IN DIATOMS AND CHROMERIDS a process called endosymbiotic gene transfer, EGT) during the evolution of plastids (Weeden Diatoms are a speciose group of unicellular al- 1981; Martin et al. 1998). These transfer events gae belonging to the phylum Stramenopila or are not restricted to plastid endosymbioses— Heterokonta, whereas chromerids are a recently the same phenomenon occurred during the en- discovered group of algae closely related to the dosymbiosis that gave rise to the mitochondria Apicomplexa (Moore et al. 2008). Thanks to the (Gray et al. 1999; Burger et al. 2003). availability of complete genome sequences or of EGT genes may serve to study the evolution- transcriptome data, recent studies have tried to ary history of plastids and, in particular, the identify EGTs in these organisms. In the case of presence of cryptic endosymbioses. In fact, spe- diatoms, a phylogenomic survey performed by cies that had a plastid in the past but lost pho- Moustafa et al. (2009) detected 4956 putative tosynthesis may have conserved genes of plastid EGTs in the genomes of the species Thalassiosira 2 Cite this article as Cold Spring Harb Perspect Biol 2014;6:a016014 Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Endosymbiotic Gene Transfer in Photosynthetic Eukaryotes pseudonana (2533 cases) and Phaeodactylum the idea that the green signal did not reveal true tricornutum (2423 cases). Such a large number green algal ancestry but just the lack of a sam- of EGTs was not necessarily surprising because, pling of red algal genes as rich as the one avail- for example, thousands of genes of presumed able for green algae and plants. Woehle et al. cyanobacterial origin have been seen in Arabi- (2011) thus concluded that improving the tax- dopsis thaliana (Martin et al. 2002). However, onomic sampling of red algae should continue the origin of most of those EGTs in diatoms to erase the green signal observed in Chromera was completely unexpected. More than 70% of and, likely, also in diatoms. them appeared to be more closely related to green algal and plant homologs than to red algal A PROBLEM OF TAXONOMIC SAMPLING ... ones. This was astonishing because diatom plas- AND METHODS tids are widely accepted to be derived from a red algal endosymbiont, and, thus, EGTs should be The work by Woehle et al. showed the impor- related to red algal homologs. To explain their tance of taxonomic sampling for the accurate results, Moustafa et al. proposed that diatoms, characterization of EGTevents. This was a clear and perhaps other related phyla, originally ac- problem in the work of Moustafa and colleagues quired a plastid by the endosymbiosis of a green on diatoms. They compared all proteins en- alga, which was secondarily replaced by the red coded by two diatom genomes (T. pseudonana algal plastid found today. and P.tricornutum) against a local sequence da- In the case of chromerids, Woehle et al. tabase that, concerning the Archaeplastida, con- (2011) analyzed expressed