Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Type Article
Date 2017-08
Language English
Author(s) Alberti Adriana1, Poulain JulieORCID1, Engelen StefanORCID1, Labadie Karine1, Romac Sarah2, 3, Ferrera IsabelORCID4, Albini Guillaume1, Aury Jean-MarcORCID1, Belser CarolineORCID1, Bertrand Alexis1, Cruaud Corinne1, Da Silva Corinne1, Dossat Carole1, Gavory FrederickORCID1, Gas Shahinaz1, Guy Julie1, Haquelle Maud1, Jacoby E'Krame1, Jaillon Olivier1, 5, 6, Lemainque Arnaud1, Pelletier Eric1, 5, Samson Gaelle1, Wessner Mark1, Acinas Silvia G.4, Royo-Llonch MartaORCID4, Cornejo-Castillo Francisco M.ORCID4, Logares RamiroORCID4, Fernandez-Gomez BeatrizORCID4, 7, 8, Bowler ChrisORCID9, Cochrane GuyORCID10, Amid ClaraORCID10, Ten Hoopen Petra10, de Vargas Colomban, Grimsley NigelORCID11, 12, Desgranges Elodie11, 12, Kandels-Lewis Stefanie13, 14, Ogata Hiroyuki15, Poulton NicoleORCID16, Sieracki Michael E.16, 17, Stepanauskas RamunasORCID16, Sullivan Matthew B.18, 19, Brum Jennifer R.19, 26, Duhaime Melissa B.20, Poulos Bonnie T.21, Hurwitz Bonnie L.22, Pesant Stephane23, 24, Karsenti Eric9, 25, Wincker Patrick1, 5, 6, Bork Peer14, 27, 28, 29, Boss EmmanuelORCID30, Follows Michael31, Gorsky Gabriel25, Hingamp PascalORCID32, Iudicone Daniele33, Karp-Boss Lee, Not Fabrice3, Raes Jeroen34, 35, Sardet Christian25, 36, Speich SabrinaORCID37, 38, Stemmann Lars25, Sunagawa ShinichiORCID14, 39, Bazire Pascal, Beluche Odette, Besnard-Gonnet Marielle, Bordelais Isabelle, Boutard Magali, Dubois Maria, Dumont Corinne, Ettedgui Evelyne, Fernandez Patricia, Garcia Esperance, Aiach Nathalie Giordanenco, Guerin Thomas, Hamon Chadia, Brun Elodie, Lebled Sandrine, Lenoble Patricia, Louesse Claudine, Mahieu Eric, Mairey Barbara, Martins Nathalie, Megret Catherine, Milani Claire, Muanga Jacqueline, Orvain Celine, Payen Emilie, Perroud Peggy, Petit Emmanuelle, Robert Dominique, Ronsin Murielle, Vacherie Benoit
Affiliation(s) 1 : CEA Inst Biol Francois Jacob, Genoscope, 2 Gaston Cremieux, F-91057 Evry, France.
2 : CNRS, Stn Biolog Roscoff, UMR 7144, Pl Georges Teissier, F-29680 Roscoff, France.
3 : Sorbonne Univ, UPMC Univ Paris 06, Stn Biolog Roscoff, UMR 7144, Pl Georges Teissier, F-29680 Roscoff, France.
4 : Inst Marine Sci ICM, Dept Biol Marina Oceanografia, CSIC, E-08003 Barcelona, Spain.
5 : CNRS, UMR 8030, CP5706, Evry, France.
6 : Univ Evry, UMR 8030, CP5706, Evry, France.
7 : FONDAP Ctr Genome Regulat, Moneda 1375, Santiago 8320000, Chile.
8 : Univ Chile, INTA, Lab Bioinformat & Expres Gen, Av El Libano, Santiago 5524, Chile.
9 : PSL Res Univ, CNRS UMR 8197,INSERM U1024, IBENS, Ecole Normale Super, 46 rue Ulm, F-75005 Paris, France.
10 : European Bioinformat Inst, European Mol Biol Lab, Wellcome Genomes Campus, Cambridge CB10 1SD, England.
11 : CNRS UMR 7232, BIOM, Ave Pierre Fabre, F-66650 Banyuls Sur Mer, France.
12 : Univ Paris 06, Sorbonne Univ, OOB UPMC, Ave Pierre Fabre, F-66650 Banyuls Sur Mer, France.
13 : Directors Res European Mol Biol Lab, Meyerhofstr 1, D-69117 Heidelberg, Germany.
14 : European Mol Biol Lab, Struct & Computat Biol, Meyerhofstr 1, D-69117 Heidelberg, Germany.
15 : Kyoto Univ, Inst Chem Res, Gokasho, Uji, Kyoto 6110011, Japan.
16 : Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
17 : Natl Sci Fdn, Arlington, VA 22230 USA.
18 : Ohio State Univ, Dept Microbiol & Civil Environm & Geodet Engn, Columbus, OH 43210 USA.
19 : Ohio State Univ, Dept Microbiol, Columbus, OH 43210 USA.
20 : Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
21 : Univ Arizona, Tucson, AZ 85721 USA.
22 : Univ Arizona, Dept Agr & Biosystems Engn, Tucson, AZ 85719 USA.
23 : Univ Bremen, Ctr Marine Environm Sci, MARUM, Leobener Str 8, D-28359 Bremen, Germany.
24 : Univ Bremen, PANGAEA, Data Publisher Earth & Environm Sci, Leobener Str 8, D-28359 Bremen, Germany.
25 : Univ Paris 06, Sorbonne Univ, UPMC,CNRS, LOV, F-06230 Villefranche Sur Mer, France.
26 : Louisiana State Univ, Dept Oceanog & Coastal Sci, Baton Rouge, LA USA.
27 : Univ Heidelberg & European Mol Biol Lab, Mol Med Partnership Unit, D-69120 Heidelberg, Germany.
28 : Max Delbruck Ctr, Mol Med, D-13125 Berlin, Germany.
29 : Univ Wurzburg, Dept Bioinformat, D-97074 Wurzburg, Germany.
30 : Univ Maine, Sch Marine Sci, Orono, ME 04469 USA.
31 : MIT, Dept Earth, Atmospher & Planetary Sci, 77 Massachusetts Ave Bldg 54, Cambridge, MA 02139 USA.
32 : Aix Marseille Univ, Univ Toulon, CNRS,IRD,MIO, OCEANOMED Batiment Mediterranee, Campus Luminy, F-13288 Marseille, France.
33 : Stazione Zoolog Anton Dohrn, Villa Comunale, I-80121 Naples, Italy.
34 : Rega Inst, Dept Microbiol & Immunol, KU Leuven, B-3000 Leuven, Belgium.
35 : VIB, Ctr Microbiol, Herestraat 49, B-3000 Leuven, Belgium.
36 : CNRS, UMR 7009 Biodev, Observatoire Oceanolog, F-06230 Villefranche Sur Mer, France.
37 : UBO IUEM, Lab Phys Oceans, Pl Copernic, F-29820 Plouzane, France.
38 : Ecole Normale Superieure, LMD, Dept Geosciences, 24 rue Lhomond, F-05 Paris, France.
39 : Inst Microbiol, Dept Biol, Vladimir Prelog Weg 4, CH-8093 Zurich, Switzerland.
Source Scientific Data (2052-4463) (Nature Publishing Group), 2017-08 , Vol. 4 , N. 170093 , P. 20p.
DOI 10.1038/sdata.2017.93
WOS© Times Cited 61
Abstract

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www. ebi. ac. uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

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Alberti Adriana, Poulain Julie, Engelen Stefan, Labadie Karine, Romac Sarah, Ferrera Isabel, Albini Guillaume, Aury Jean-Marc, Belser Caroline, Bertrand Alexis, Cruaud Corinne, Da Silva Corinne, Dossat Carole, Gavory Frederick, Gas Shahinaz, Guy Julie, Haquelle Maud, Jacoby E'Krame, Jaillon Olivier, Lemainque Arnaud, Pelletier Eric, Samson Gaelle, Wessner Mark, Acinas Silvia G., Royo-Llonch Marta, Cornejo-Castillo Francisco M., Logares Ramiro, Fernandez-Gomez Beatriz, Bowler Chris, Cochrane Guy, Amid Clara, Ten Hoopen Petra, de Vargas Colomban, Grimsley Nigel, Desgranges Elodie, Kandels-Lewis Stefanie, Ogata Hiroyuki, Poulton Nicole, Sieracki Michael E., Stepanauskas Ramunas, Sullivan Matthew B., Brum Jennifer R., Duhaime Melissa B., Poulos Bonnie T., Hurwitz Bonnie L., Pesant Stephane, Karsenti Eric, Wincker Patrick, Bork Peer, Boss Emmanuel, Follows Michael, Gorsky Gabriel, Hingamp Pascal, Iudicone Daniele, Karp-Boss Lee, Not Fabrice, Raes Jeroen, Sardet Christian, Speich Sabrina, Stemmann Lars, Sunagawa Shinichi, Bazire Pascal, Beluche Odette, Besnard-Gonnet Marielle, Bordelais Isabelle, Boutard Magali, Dubois Maria, Dumont Corinne, Ettedgui Evelyne, Fernandez Patricia, Garcia Esperance, Aiach Nathalie Giordanenco, Guerin Thomas, Hamon Chadia, Brun Elodie, Lebled Sandrine, Lenoble Patricia, Louesse Claudine, Mahieu Eric, Mairey Barbara, Martins Nathalie, Megret Catherine, Milani Claire, Muanga Jacqueline, Orvain Celine, Payen Emilie, Perroud Peggy, Petit Emmanuelle, Robert Dominique, Ronsin Murielle, Vacherie Benoit (2017). Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Scientific Data, 4(170093), 20p. Publisher's official version : https://doi.org/10.1038/sdata.2017.93 , Open Access version : https://archimer.ifremer.fr/doc/00600/71256/