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Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus

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Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus Genome analysis of the smallest free-living eukaryote SEE COMMENTARY Ostreococcus tauri unveils many unique features Evelyne Derellea,b, Conchita Ferrazb,c, Stephane Rombautsb,d, Pierre Rouze´ b,e, Alexandra Z. Wordenf, Steven Robbensd, Fre´ de´ ric Partenskyg, Sven Degroeved,h, Sophie Echeynie´ c, Richard Cookei, Yvan Saeysd, Jan Wuytsd, Kamel Jabbarij, Chris Bowlerk, Olivier Panaudi, BenoıˆtPie´ gui, Steven G. Ballk, Jean-Philippe Ralk, Franc¸ois-Yves Bougeta, Gwenael Piganeaua, Bernard De Baetsh, Andre´ Picarda,l, Michel Delsenyi, Jacques Demaillec, Yves Van de Peerd,m, and Herve´ Moreaua,m aObservatoire Oce´anologique, Laboratoire Arago, Unite´Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France; cInstitut de Ge´ne´ tique Humaine, Unite´Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France; dDepartment of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and eLaboratoire Associe´de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, 9052 Ghent, Belgium; fRosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149; gStation Biologique, Unite´Mixte de Recherche 7144, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP74, 29682 Roscoff Cedex, France; hDepartment of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; iGe´nome et De´veloppement des Plantes, Unite´Mixte de Recherche 5096, Centre National de la Recherche Scientifique–Universite´de Perpignan, 52, Avenue de Villeneuve, 66860 Perpignan, France; jDe´partement de Biologie, Formation de Recherche en Evolution 2910, Centre National de la Recherche Scientifique–Ecole Normale Supe´rieure, 46 Rue d’Ulm, 75230 Paris Cedex 05, France; and kLaboratoire de Chimie Biologique, Unite´Mixte de Recherche 8765, Centre National de la Recherche Scientifique–Universite´Sciences et Technologies de Lille, 59655 Villeneuve d’Ascq, France Communicated by Marc C. E. Van Montagu, Ghent University, Ghent, Belgium, June 8, 2006 (received for review January 4, 2006) The green lineage is reportedly 1,500 million years old, evolving having disposed of redundancies and presenting a simple organi- shortly after the endosymbiosis event that gave rise to early zation and very little noncoding sequence. photosynthetic eukaryotes. In this study, we unveil the complete Since its identification in 1994, Ostreococcus has been recognized genome sequence of an ancient member of this lineage, the as a common member of the natural marine phytoplankton assem- unicellular green alga Ostreococcus tauri (Prasinophyceae). This blage. It is cosmopolitan in distribution, having been found from cosmopolitan marine primary producer is the world’s smallest coastal to oligotrophic waters, including the English Channel, the free-living eukaryote known to date. Features likely reflecting Mediterranean and Sargasso Seas, and the North Atlantic, Indian, optimization of environmentally relevant pathways, including re- and Pacific Oceans (7–12). Eukaryotes within the picosize fraction Ͻ ␮ source acquisition, unusual photosynthesis apparatus, and genes ( 2- to 3- m diameter) have been shown to contribute significantly potentially involved in C photosynthesis, were observed, as was to marine primary production (9, 13). Ostreococcus itself is notable 4 for its rapid growth rates and potential grazer susceptibility (9, 14). downsizing of many gene families. Overall, the 12.56-Mb nuclear Furthermore, dramatic blooms of this organism have been re- genome has an extremely high gene density, in part because of corded off the coasts of Long Island (15) and California (11). At the extensive reduction of intergenic regions and other forms of same time, attention has focused on the tremendous diversity of compaction such as gene fusion. However, the genome is struc- picoeukaryotes (16, 17), which holds true for Ostreococcus as well. turally complex. It exhibits previously unobserved levels of heter- Recently, Ostreococcus strains isolated from surface waters were ogeneity for a eukaryote. Two chromosomes differ structurally shown to represent genetically and physiologically distinct ecotypes, from the other eighteen. Both have a significantly biased G؉C with light-regulated growth optima different from those isolated content, and, remarkably, they contain the majority of transpos- from the deep chlorophyll maximum (18). These findings are able elements. Many chromosome 2 genes also have unique codon similar to the niche adaptations documented in different ecotypes usage and splicing, but phylogenetic analysis and composition do of the abundant marine cyanobacteria Prochlorococcus (19, 20). not support alien gene origin. In contrast, most chromosome 19 Overall, marine picophytoplankton play a significant role in genes show no similarity to green lineage genes and a large primary productivity and food webs, especially in oligotrophic number of them are specialized in cell surface processes. Taken environments where they account for up to 90% of the autotrophic together, the complete genome sequence, unusual features, and biomass (9, 13, 21, 22). Several recent studies have undertaken a downsized gene families, make O. tauri an ideal model system for genome sequencing approach to understand the ocean ecology of research on eukaryotic genome evolution, including chromosome phytoplankton. To date, these studies have focused on the bacterial GENETICS specialization and green lineage ancestry. component of the plankton, particularly on the picocyanobacteria Prochlorococcus (20) and Synechococcus (23), for which 9 complete genome heterogeneity ͉ genome sequence ͉ green alga ͉ Prasinophyceae ͉ gene prediction Conflict of interest statement: No conflicts declared. Abbreviation: TE, transposable element. he smallest free-living eukaryote known so far is Ostreococcus Data deposition: The genome data have been submitted to the European Molecular Ttauri (1). This tiny unicellular green alga belongs to the Prasi- Biology Laboratory, www.embl.org [accession nos. CR954201 (Chrom 1), CR954202 (Chrom nophyceae, one of the most ancient groups (2) within the lineage 2), CR954203 (Chrom 3), CR954204 (Chrom 4), CR954205 (Chrom 5), CR954206 (Chrom 6), giving rise to the green plants currently dominating terrestrial CR954207 (Chrom 7), CR954208 (Chrom 8), CR954209 (Chrom 9), CR954210 (Chrom10), CR954211 (Chrom 11), CR954212 (Chrom 12), CR954213 (Chrom 13), CR954214 (Chrom 14), photosynthesis (the green lineage) (3, 4). Consequently, since its CR954215 (Chrom 15), CR954216 (Chrom 16), CR954217 (Chrom 17), CR954218 (Chrom 18), discovery, there has been great interest in O. tauri, which, because CR954219 (Chrom 19), and CR954220 (Chrom 20)]. of its apparent overall simplicity, a naked, nonflagellated cell See Commentary on page 11433. possessing a single mitochondrion and chloroplast, in addition to its bE.D., C.F., S.R., and P.R. contributed equally to this work. small size and ease in culturing, renders it an excellent model lDeceased November 21, 2004. organism (5). Furthermore, it has been hypothesized, based on its mTo whom correspondence may be addressed. E-mail: [email protected] or small cellular and genome sizes (2, 6), that it may reveal the ‘‘bare [email protected]. limits’’ of life as a free-living photosynthetic eukaryote, presumably © 2006 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0604795103 PNAS ͉ August 1, 2006 ͉ vol. 103 ͉ no. 31 ͉ 11647–11652 Downloaded by guest on January 8, 2020 Fig. 1. General characteristics of the 20 O. tauri chromosomes. TEs, transposon frequency. Size is indicated to the left of each chromosome (Mb). Colored bars indicate the percentage GϩC content (upper bar) and of transposons (lower bar). genome sequences are already publicly available and Ͼ13 others on content of O. tauri is more akin to that of C. merolae than to that the way. Much less is known about eukaryotic phytoplankton, of plants, fungi, or even T. pseudonana (Table 1). As shown in Fig. because only one, the diatom Thalassiosira pseudonana, has a 2 and Table 1, 8,166 protein-coding genes were predicted in the complete genome sequenced (24). Picoeukaryotes are especially nuclear genome, making O. tauri the most gene dense free-living interesting in the context of marine primary production, given the eukaryote known to date. Only the chromosomes of the nucleo- combination of their broad environmental distribution and the fact morphs within chlorachniophyte and cryptophyte algae are more that their surface area to volume ratio, a critical factor in resource gene-dense bodies (27), which are internally contained and not acquisition and success in oligotrophic environments (25), is similar capable of independent propagation. We found that 6,265 genes are to that of prokaryotic counterparts generally considered superior in supported by homology with known genes in public databases Ϫ uptake and transport of nutrients. (e-value Ͻ10 5), of which the majority (46%) were most similar to In this article, we describe the complete genome sequence of O. plant orthologs (Fig. 3). Very few repeated sequences have been tauri OTH95, a strain isolated in the Thau lagoon (France) in which found in this genome, except for a long internal
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