Abstract
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
| Originalsprog | Engelsk |
|---|---|
| Artikelnummer | 100123 |
| Tidsskrift | Cell Genomics |
| Vol/bind | 2 |
| Udgave nummer | 5 |
| Antal sider | 17 |
| ISSN | 2666-979x |
| DOI | |
| Status | Udgivet - 2022 |
Bibliografisk note
Funding Information:Our survey was made possible by two scientific endeavors: the sampling and sequencing efforts by the Tara Oceans Project and the bioinformatics and visualization capabilities afforded by anvi’o. We are indebted to all who contributed to these efforts, as well as other open-source bioinformatics tools for their commitment to transparency and openness. Tara Oceans (which includes the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean Foundation and the continuous support of 23 institutes ( https://oceans.taraexpeditions.org/ ). We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the Study of Global Ocean Systems Ecology and Evolution FR2022/Tara GOSEE ), the European Molecular Biology Laboratory (EMBL), Genoscope/CEA , the French Ministry of Research and the French Governement ‘Investissement d’Avenir’ programs Oceanomics ( ANR-11-BTBR-0008 ), FRANCE GENOMIQUE ( ANR-10-INBS-09 ), ATIGE Genopole postdoctoral fellowship, HYDROGEN / ANR-14-CE23-0001 , MEMO LIFE ( ANR-10-LABX-54 ), PSL Research University ( ANR-11-IDEX-0001-02 ) and EMBRC-France ( ANR-10-INBS-02 ), Fund for Scientific Research—Flanders , VIB , Stazione Zoologica Anton Dohrn , UNIMIB , ANR (projects ALGALVIRUS ANR-17-CE02- 0012 , PHYTBACK/ANR-2010-1709-01 , POSEIDON/ANR-09-BLAN-0348 , PROMETHEUS/ANR-09-PCS-GENM-217 , TARA-GIRUS/ANR-09-PCS-GENM-218 ), EU FP7 ( MicroB3/No. 287589 , IHMS/HEALTH-F4-2010-261376 ), Genopole , CEA DRF Impulsion program, OCEANOMICS (project no. ANR-11-BTBR-0008), ERC Advanced Award Diatomic (grant agreement No 835067) to CB. The authors also thank Agnès B. and E. Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, the EDF Foundation, Region Bretagne, Lorient Agglomeration, Worldcourier, Illumina, Serge Ferrari, and the Fonds Francais pour l'Environnement Mondial for support and commitment. The global sampling effort was made possible by countless scientists and crew who performed sampling aboard the Tara from 2009 to 2013. The authors are also grateful to the countries that graciously granted sampling permission. Part of the computations were performed using the platine, titane, and curie HPC machine provided through GENCI grants ( t2011076389 , t2012076389 , t2013036389 , t2014036389 , t2015036389 , and t2016036389 ). We also thank Noan Le Bescot (TernogDesign) for artwork on figures.
Funding Information:
Our survey was made possible by two scientific endeavors: the sampling and sequencing efforts by the Tara Oceans Project and the bioinformatics and visualization capabilities afforded by anvi'o. We are indebted to all who contributed to these efforts, as well as other open-source bioinformatics tools for their commitment to transparency and openness. Tara Oceans (which includes the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org/). We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the Study of Global Ocean Systems Ecology and Evolution FR2022/Tara GOSEE), the European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Ministry of Research and the French Governement ‘Investissement d'Avenir’ programs Oceanomics (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09), ATIGE Genopole postdoctoral fellowship, HYDROGEN/ANR-14-CE23-0001, MEMO LIFE (ANR-10-LABX-54), PSL Research University (ANR-11-IDEX-0001-02) and EMBRC-France (ANR-10-INBS-02), Fund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects ALGALVIRUS ANR-17-CE02- 0012, PHYTBACK/ANR-2010-1709-01, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No. 287589, IHMS/HEALTH-F4-2010-261376), Genopole, CEA DRF Impulsion program, OCEANOMICS (project no. ANR-11-BTBR-0008), ERC Advanced Award Diatomic (grant agreement No 835067) to CB. The authors also thank Agnès B. and E. Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, the EDF Foundation, Region Bretagne, Lorient Agglomeration, Worldcourier, Illumina, Serge Ferrari, and the Fonds Francais pour l'Environnement Mondial for support and commitment. The global sampling effort was made possible by countless scientists and crew who performed sampling aboard the Tara from 2009 to 2013. The authors are also grateful to the countries that graciously granted sampling permission. Part of the computations were performed using the platine, titane, and curie HPC machine provided through GENCI grants (t2011076389, t2012076389, t2013036389, t2014036389, t2015036389, and t2016036389). We also thank Noan Le Bescot (TernogDesign) for artwork on figures. D.D.H. M.G. E.P. P.W. O.J. and T.O.D. conducted the study. T.O.D. and M.G. characterized the MAGs and SAGs, and RNA polymerase genes, respectively. D.D.H. (analysis of the ∼10 million genes), M.G. (phylogenies), P.F. (climate models and world map projections), E.P. (METdb database, mapping results), and T.O.D. performed the primary analysis of the data. A.K. L.d.A. Q.C. and J.-M.A. assembled and annotated the single cell genomes and helped to process metagenomic assemblies. E.V. M.W. B.N. C.D.S. D.D.H. O.J. and J.-M.A. identified the eukaryotic genes in the MAG assemblies. A.F.G. and C.V. characterized the repertoire of functions in the unknown coding sequence space. T.O.D. wrote the manuscript with critical inputs from all the authors. This article is contribution number 132 of Tara Oceans. The authors declare no competing interests.
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