A global ocean atlas of eukaryotic genes

Type Article
Date 2018-01
Language English
Author(s) Carradec QuentinORCID1, 2, 3, Pelletier EricORCID1, 2, 3, Da Silva Corinne1, Alberti AdrianaORCID1, Seeleuthner Yoann1, 2, 3, Blanc-Mathieu RomainORCID4, Lima-Mendez GipsiORCID5, 6, 23, 24, Rocha Fabio7, Tirichine Leila7, Labadie Karine1, Kirilovsky Amos1, 2, 3, 7, Bertrand Alexis1, Engelen StefanORCID1, Madoui Mohammed-AminORCID1, 2, 3, Meheust RaphaelORCID7, Poulain JulieORCID1, Romac Sarah8, 9, 13, Richter Daniel J.8, 9, Yoshikawa Genki4, Dimier Celine7, 8, 9, Kandels-Lewis Stefanie10, 11, Picheral Marc12, Searson Sarah, Jaillon OlivierORCID1, 2, 3, Aury Jean-MarcORCID1, Karsenti Eric7, 11, 12, Sullivan Matthew B.14, 15, Sunagawa ShinichiORCID10, 16, Bork Peer10, 17, 18, 19, 20, Not Fabrice8, 9, Hingamp PascalORCID21, Raes Jeroen5, 6, Guidi LionelORCID12, 13, Ogata Hiroyuki4, de Vargas Colomban8, 9, Iudicone Daniele22, Bowler ChrisORCID7, Wincker Patrick1, 2, 3, Tara Oceans Coordinators
Contributor(s) Speich Sabrina
Affiliation(s) 1 : CEA, Inst Biol Francois Jacob, Genoscope, F-91057 Evry, France.
2 : CNRS, UMR Metab Genom, F-91057 Evry, France.
3 : Univ Evry, F-91057 Evry, France.
4 : Kyoto Univ, Inst Chem Res, Uji, Kyoto 6110011, Japan.
5 : Katholieke Univ Leuven, Rega Inst, Dept Microbiol & Immunol, Herestr 49, B-3000 Leuven, Belgium.
6 : VIB Ctr Microbiol, Herestr 49, B-3000 Leuven, Belgium.
7 : PSL Res Univ, Ecole Normale Super, IBENS, CNRS UMR 8197,INSERM,U1024, 46 Rue Ulm, F-75005 Paris, France.
8 : CNRS, UMR 7144, Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
9 : UPMC Univ Paris 06, Sorbonne Univ, Stn Biol Roscoff, UMR 7144, Pl Georges Teissier, F-29680 Roscoff, France.
10 : European Mol Biol Lab, Struct & Computat Biol, Meyerhofstr 1, D-69117 Heidelberg, Germany.
11 : European Mol Biol Lab, Directors Res, Meyerhofstr 1, D-69117 Heidelberg, Germany.
12 : UPMC Univ Paris 06, CNRS, Sorbonne Univ, LOV,Observ Oceanol, F-06230 Villefranche Sur Mer, France.
13 : Univ Hawaii, Dept Oceanog, Honolulu, HI 96844 USA.
14 : Ohio State Univ, Dept Microbiol, Columbus, OH 43210 USA.
15 : Ohio State Univ, Dept Civil Environm & Geodet Engn, Columbus, OH 43210 USA.
16 : Inst Microbiol, Dept Biol, Vladimir Prelog Weg 4, CH-8093 Zurich, Switzerland.
17 : Heidelberg Univ, Mol Med Partnership Unit, D-69120 Heidelberg, Germany.
18 : European Mol Biol Lab, D-69120 Heidelberg, Germany.
19 : Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany.
20 : Univ Wurzburg, Dept Bioinformat, D-97074 Wurzburg, Germany.
21 : Univ Toulon & Var, Aix Marseille Univ, CNRS, IRD,MIO, F-13284 Marseille, France.
22 : Villa Comunale, Stn Zool Anton Dohrn, I-80121 Naples, Italy.
23 : Univ Libre Bruxelles, Fac Sci, Cellular & Mol Microbiol, Brussels, Belgium.
24 : ULB VUB, Interuniv Inst Bioinformat Brussels, Blvd Triomphe CP 263, B-1050 Brussels, Belgium.
Source Nature Communications (2041-1723) (Nature Publishing Group), 2018-01 , Vol. 9 , N. 373 , P. 13p.
DOI 10.1038/s41467-017-02342-1
WOS© Times Cited 96
Abstract

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.

Full Text
File Pages Size Access
Publisher's official version 13 2 MB Open access
Supplementary Information 14 2 MB Open access
Description of Additional Supplementary Files 1 174 KB Open access
Supplementary Data 1 9 KB Open access
Supplementary Data 2 11 KB Open access
Supplementary Data 3 9 KB Open access
Supplementary Data 4 9 KB Open access
Supplementary Data 5 137 KB Open access
Supplementary Data 6 71 KB Open access
Supplementary Data 7 34 KB Open access
Supplementary Data 8 126 KB Open access
Top of the page

How to cite 

Carradec Quentin, Pelletier Eric, Da Silva Corinne, Alberti Adriana, Seeleuthner Yoann, Blanc-Mathieu Romain, Lima-Mendez Gipsi, Rocha Fabio, Tirichine Leila, Labadie Karine, Kirilovsky Amos, Bertrand Alexis, Engelen Stefan, Madoui Mohammed-Amin, Meheust Raphael, Poulain Julie, Romac Sarah, Richter Daniel J., Yoshikawa Genki, Dimier Celine, Kandels-Lewis Stefanie, Picheral Marc, Searson Sarah, Jaillon Olivier, Aury Jean-Marc, Karsenti Eric, Sullivan Matthew B., Sunagawa Shinichi, Bork Peer, Not Fabrice, Hingamp Pascal, Raes Jeroen, Guidi Lionel, Ogata Hiroyuki, de Vargas Colomban, Iudicone Daniele, Bowler Chris, Wincker Patrick, Tara Oceans Coordinators (2018). A global ocean atlas of eukaryotic genes. Nature Communications, 9(373), 13p. Publisher's official version : https://doi.org/10.1038/s41467-017-02342-1 , Open Access version : https://archimer.ifremer.fr/doc/00660/77232/