TY - JOUR
T1 - A global ocean atlas of eukaryotic genes
AU - Tara Oceans Coordinators
AU - Carradec, Quentin
AU - Pelletier, Eric
AU - Da Silva, Corinne
AU - Alberti, Adriana
AU - Seeleuthner, Yoann
AU - Blanc-Mathieu, Romain
AU - Lima-Mendez, Gipsi
AU - Rocha, Fabio
AU - Tirichine, Leila
AU - Labadie, Karine
AU - Kirilovsky, Amos
AU - Bertrand, Alexis
AU - Engelen, Stefan
AU - Madoui, Mohammed Amin
AU - Méheust, Raphaël
AU - Poulain, Julie
AU - Romac, Sarah
AU - Richter, Daniel J.
AU - Yoshikawa, Genki
AU - Dimier, Céline
AU - Kandels-Lewis, Stefanie
AU - Picheral, Marc
AU - Searson, Sarah
AU - Acinas, Silvia G.
AU - Boss, Emmanuel
AU - Follows, Michael
AU - Gorsky, Gabriel
AU - Grimsley, Nigel
AU - Karp-Boss, Lee
AU - Krzic, Uros
AU - Pesant, Stephane
AU - Reynaud, Emmanuel G.
AU - Sardet, Christian
AU - Sieracki, Mike
AU - Speich, Sabrina
AU - Stemmann, Lars
AU - Velayoudon, Didier
AU - Weissenbach, Jean
AU - Jaillon, Olivier
AU - Aury, Jean Marc
AU - Karsenti, Eric
AU - Sullivan, Matthew B.
AU - Sunagawa, Shinichi
AU - Bork, Peer
AU - Not, Fabrice
AU - Hingamp, Pascal
AU - Raes, Jeroen
AU - Guidi, Lionel
AU - Ogata, Hiroyuki
AU - De Vargas, Colomban
N1 - Funding Information:
We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Governement 'Investissement d'Avenir' programs Oceanomics (ANR-11-BTBR-0008), MEMO LIFE (ANR-10-LABX-54), PSL Research University (ANR-11-IDEX-0001-02), and France GENOMIQUE (ANR-10-INBS-09), Fund for Scientific Research-Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects 'PHYTBACK/ANR-2010-1709-01', POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCSGENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No.287589), ERC Advanced Grant Award (Diatomite: 294823), the LouisD foundation of the Institut de France, a Radcliffe Institute Fellowship from Harvard University to CB, JSPS/MEXT KAKENHI (Nos. 26430184, 16H06437, 16H06429, 16K21723, 16KT0020), The Canon Foundation (No. 203143100025), agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner, and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org). We also acknowledge C. Scarpelli for support in high-performance computing. Computations were performed using the platine, titane and curie HPC machine provided through GENCI grants (t2011076389, t2012076389, t2013036389, t2014036389, t2015036389, and t2016036389). This article is contribution number 62 of Tara Oceans.
Funding Information:
We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Governe-ment ‘Investissement d’Avenir’ programs Oceanomics (ANR-11-BTBR-0008), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001–02), and FRANCE GENOMIQUE (ANR-10-INBS-09), Fund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects ‘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), ERC Advanced Grant Award (Diatomite: 294823), the LouisD foundation of the Institut de France, a Radcliffe Institute Fellowship from Harvard University to CB, JSPS/MEXT KAKENHI (Nos. 26430184, 16H06437, 16H06429, 16K21723, 16KT0020), The Canon Foundation (No. 203143100025), agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner, and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org). We also acknowledge C. Scarpelli for support in high-performance computing. Computations were performed using the platine, titane and curie HPC machine provided through GENCI grants (t2011076389, t2012076389, t2013036389, t2014036389, t2015036389, and t2016036389). This article is contribution number 62 of Tara Oceans.
Publisher Copyright:
© 2018 The Author(s).
PY - 2018/12/1
Y1 - 2018/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85041090483&partnerID=8YFLogxK
U2 - 10.1038/s41467-017-02342-1
DO - 10.1038/s41467-017-02342-1
M3 - Article
C2 - 29371626
AN - SCOPUS:85041090483
SN - 2041-1723
VL - 9
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 373
ER -