The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation Brian Palenika,b, Jane Grimwoodc, Andrea Aertsd, Pierre Rouze´ e, Asaf Salamovd, Nicholas Putnamd, Chris Duponta, Richard Jorgensenf, Evelyne Derelleg, Stephane Rombautsh, Kemin Zhoud, Robert Otillard, Sabeeha S. Merchanti, Sheila Podellj, Terry Gaasterlandj, Carolyn Napolif, Karla Gendlerf, Andrea Manuellk, Vera Taia, Olivier Vallonl, Gwenael Piganeaug,Se´ verine Jancekg, Marc Heijdem, Kamel Jabbarim, Chris Bowlerm, Martin Lohrn, Steven Robbensh, Gregory Wernerd, Inna Dubchakd, Gregory J. Pazouro, Qinghu Renp, Ian Paulsenp, Chuck Delwicheq, Jeremy Schmutzc, Daniel Rokhsard, Yves Van de Peerh, Herve´ Moreaug, and Igor V. Grigorievb,d aScripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202; cJoint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304; dU.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598; eLaboratoire Associe´de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; fDepartment of Plant Sciences, University of Arizona, 303 Forbes Building, Tucson, AZ 85721-0036; gObservatoire Oce´anologique, Laboratoire Arago, Centre National de la Recherche Scientifique/Universite´Pierre et Marie Curie Paris 6, Unite´Mixte de Recherche 7628, BP 44, 66651 Banyuls sur Mer Cedex, France; hDepartment of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; iDepartment of Chemistry and Biochemistry, University of California, Box 951569, Los Angeles, CA 90095; jScripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202; kDepartment of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; lInstitut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique/Universite´Paris 6, Unite´Mixte de Recherche 7141, 13, Rue Pierre et Marie Curie, 75005 Paris, France; mDe´partement de Biologie, Ecole Normale Supe´rieure, Formation de Recherche en Evolution 2910, Centre National de la Recherche Scientifique, 46, Rue D’Ulm, 75230 Paris Cedex 05, France; nInstitut fu¨r Allgemeine Botanik, Johannes Gutenberg-Universita¨t, D-55099 Mainz, Germany; oProgram in Molecular Medicine, University of Massachusetts Medical School, Suite 213, Biotech II, 373 Plantation Street, Worcester, MA 01605; pThe Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; and qCell Biology and Molecular Genetics, University of Maryland, H. J. Patterson Hall, Building 073, College Park, MD 20742-5815 Edited by Robert Haselkorn, University of Chicago, Chicago, IL, and approved March 13, 2007 (received for review December 12, 2006) The smallest known eukaryotes, at Ϸ1-␮m diameter, are Ostreo- tion, with no cell wall or flagella, and with a single chloroplast and coccus tauri and related species of marine phytoplankton. The mitochondrion (4). Recent work has shown that small-subunit genome of Ostreococcus lucimarinus has been completed and rDNA sequences of Ostreococcus from cultures and environmental compared with that of O. tauri. This comparison reveals surprising samples cluster into four different clades that are likely distinct differences across orthologous chromosomes in the two species enough to represent different species (6, 9). from highly syntenic chromosomes in most cases to chromosomes Here we report on the gene content, genome organization, and with almost no similarity. Species divergence in these phytoplank- deduced metabolic capacity of the complete genome of Ostreococ- ton is occurring through multiple mechanisms acting differently on cus sp. strain CCE9901 (7), a representative of surface–ocean different chromosomes and likely including acquisition of new adapted Ostreococcus, referred to here as Ostreococcus lucimarinus. genes through horizontal gene transfer. We speculate that this We compare it to the analogous features of the related species O. latter process may be involved in altering the cell-surface charac- tauri strain OTH95 (10). Our results show that many processes have teristics of each species. In addition, the genome of O. lucimarinus been involved in the evolution and speciation of even these sister provides insights into the unique metal metabolism of these organisms, from dramatic changes in genome structure to signifi- organisms, which are predicted to have a large number of seleno- cant differences in metabolic capabilities. cysteine-containing proteins. Selenoenzymes are more catalyti- cally active than similar enzymes lacking selenium, and thus the cell Results may require less of that protein. As reported here, selenoenzymes, Gene Content. O. lucimarinus is the first closed and finished genome novel fusion proteins, and loss of some major protein families of a green alga and as such will provide a great resource for in-depth including ones associated with chromatin are likely important analysis of genome organization and the processes of eukaryotic adaptations for achieving a small cell size. genome evolution. O. lucimarinus has a nuclear genome size of 13.2 million base pairs found in 21 chromosomes, as compared with a green algae ͉ picoeukaryote ͉ genome evolution ͉ selenium ͉ synteny genome size for O. tauri of 12.6 million base pairs found in 20 hytoplankton living in the oceans perform nearly half of total PLANT BIOLOGY Pglobal photosynthesis (1). Eukaryotic phytoplankton exhibit Author contributions: J.G. and A.A. performed research; B.P., P.R., A.S., N.P., C. Dupont, R.J., E.D., S. Rombauts, K.Z., R.O., S.S.M., S.P., T.G., C.N., K.G., A.M., V.T., O.V., G.P., S.J., M.H., K.J., great diversity that contrasts with the lower apparent diversity of C.B., M.L., S. Robbens, G.W., I.D., G.J.P., Q.R., I.P., C. Delwiche, J.S., D.R., Y.V.d.P., H.M., and ecological niches available to them in aquatic ecosystems. This I.V.G. analyzed data; and B.P., P.R., C. Dupont, R.J., K.Z., S.S.M., M.L., H.M., and I.V.G. wrote observation, know as the ‘‘paradox of the plankton,’’ has long the paper. puzzled biologists (2). By providing molecular level information on The authors declare no conflict of interest. related species, genomics is poised to provide new insights into this This article is a PNAS Direct Submission. paradox. Abbreviations: Chr n, chromosome n; GC, guanine plus cytosine. Picophytoplankton, with cell diameters Ͻ2 ␮m, play a significant Data deposition: The O. lucimarinus genome sequence, predicted genes, and annotations role in major biogeochemical processes, primary productivity, and reported in this paper have been deposited in the GenBank database (accession nos. food webs, especially in oligotrophic waters. Within this size class, CP000581–CP000601 for Chr 1 through Chr 21). The O. lucimarinus strain (CCE9901) used here has been deposited in the Provasoli-Guillard Culture Collection of Marine Phytoplank- the smallest known eukaryotes are Ostreococcus tauri and related ton (accession no. CCMP2514). species. Although more similar to flattened spheres in shape, these bTo whom correspondence may be addressed. E-mail: [email protected] or ivgrigoriev@ organisms are Ϸ1 ␮m in diameter (3, 4) and have been isolated or lbl.gov. detected from samples of diverse geographical origins (5–8). They This article contains supporting information online at www.pnas.org/cgi/content/full/ belong to the Prasinophyceae, an early diverging class within the 0611046104/DC1. green plant lineage, and have a strikingly simple cellular organiza- © 2007 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0611046104 PNAS ͉ May 1, 2007 ͉ vol. 104 ͉ no. 18 ͉ 7705–7710 Downloaded by guest on September 26, 2021 Table 1. Summary of predicted genes in Ostreococcus lucimarinus, and 7,892 genes are found in the genome of O. tauri. sp. genomes Overall gene content is similar between the genomes (Table 1). Properties O. lucimarinus O. tauri Approximately one-fifth of all genes in both genomes have mul- tiexon structure, most of which belong to chromosome 2 (Chr 2), Genome size, Mbp 13.2 12.6 and have the introns of unusual size and structure that were Chromosomes 21 20 reported earlier for O. tauri (10). A total of 6,753 pairs of orthologs No. of genes 7,651 7,892 have been identified between genes in the two Ostreococcus species Multiexon genes, % 20 25 Supported by, % with an average coverage of 93% and an average amino acid Multiple methods 28 19 identity of 70%. A comparison of the amino acid identity between Genome conservation 65 73 other sister taxa shows that they are more divergent than charac- Homology to another strain 93 92 terized species of Saccharomyces with similar levels of overall Homology to SwissProt 84 79 synteny [supporting information (SI) Table 2]. ESTs 28 21 Approximately 5–6% of gene models are genome-specific and do Peptides 13 N/D not display homology to the other species (SI Table 3). These are Average gene size, bp 1,284 1,245 mostly due to lineage-specific gene loss or acquisition or remaining Transcript size, bp 1,234 1,175 No. of exons per gene 1.27 1.57 gaps in the O. tauri sequence. The number of lineage-specific Exon size, bp 970 750 duplications is also low, 9% for O. lucimarinus and 4% for O. tauri, Intron size, bp 187 126 mostly because of several segmental duplications. N/D, not determined. Genome Structure. Based on analysis of gene content, orthology, and DNA alignments, 20 chromosomes in each genome have a counterpart in the other species. Eighteen of these 20 are highly chromosomes (10) (Table 1). For comparison here, both genomes syntenic (Fig. 1) and formed the core of the ancestral Ostreococcus were annotated by using the same tools, as described in Methods. genome. The remaining two chromosomes of O.