Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
Yoann Seeleuthner
(1, 2)
,
Samuel Mondy
(2, 3)
,
Vincent Lombard
(4)
,
Quentin Carradec
(2, 3)
,
Eric Pelletier
(2, 3)
,
Marc Wessner
(2, 3)
,
Jade Leconte
(2, 3)
,
Jean-François Mangot
(5)
,
Julie Poulain
(2)
,
Karine Labadie
(2)
,
Ramiro Logares
(6)
,
Shinichi Sunagawa
(7)
,
Véronique de Berardinis
(3, 2)
,
Marcel Salanoubat
(2, 3)
,
Céline Dimier
(8)
,
Stefanie Kandels-Lewis
(7)
,
Marc Picheral
(9, 10)
,
Sarah Searson
(11)
,
Stéphane Pesant
(12, 13)
,
Nicole Poulton
(14)
,
Ramunas Stepanauskas
(14)
,
Peer Bork
(7)
,
Chris Bowler
(8)
,
Pascal Hingamp
(15)
,
Matthew B. Sullivan
(16)
,
Daniele Iudicone
(17)
,
Ramon Massana
(6)
,
Jean-Marc Aury
(2)
,
Bernard Henrissat
(4, 18)
,
Eric Karsenti
(8, 11, 12, 13)
,
Olivier Jaillon
(2, 3)
,
Mike Sieracki
(19)
,
Colomban de Vargas
(20)
,
Patrick Wincker
(2, 3)
,
Silvia G. Acinas
(6)
,
Emmanuel Boss
(21)
,
Michael Follows
(22)
,
Gabriel Gorsky
(13)
,
Nigel Grimsley
(23)
,
Lee Karp-Boss
(21)
,
Uros Krzic
(7)
,
Fabrice Not
(20)
,
Jeroen Raes
(24)
,
Emmanuel G. Reynaud
(25)
,
Christian Sardet
(13, 26)
,
Sabrina Speich
(27, 28)
,
Lars Stemmann
(13)
,
Jean Weissenbach
(29)
,
Didier Velayoudon
(29)
1
IG -
Institut de Génomique d'Evry
2 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
3 UMR 8030 - Génomique métabolique
4 AFMB - Architecture et fonction des macromolécules biologiques
5 LMGE - Laboratoire Microorganismes : Génome et Environnement
6 ICM - Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona]
7 EMBL - European Molecular Biology Laboratory [Heidelberg]
8 IBENS - Institut de biologie de l'ENS Paris
9 LOV - Laboratoire d'océanographie de Villefranche
10 SU - Sorbonne Université
11 Department of Oceanography [Honolulu]
12 MARUM - Center for Marine Environmental Sciences [Bremen]
13 PANGAEA - Data Publisher for Earth and Environmental Science
14 Bigelow Laboratory for Ocean Sciences
15 MIO - Institut méditerranéen d'océanologie
16 OSU - Ohio State University [Columbus]
17 SZN - Stazione Zoologica Anton Dohrn
18 Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
19 NSF - National Science Foundation [Arlington]
20 ADMM - Adaptation et diversité en milieu marin
21 University of Maine
22 EAPS - Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge]
23 BIOM - Biologie intégrative des organismes marins
24 Rega Institute for Medical Research [Leuven, België]
25 UCD - University College Dublin [Dublin]
26 LBDV - Laboratoire de Biologie du Développement de Villefranche sur mer
27 LMD - Laboratoire de Météorologie Dynamique (UMR 8539)
28 UBO - Université de Brest
29 DVIP Consulting
2 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
3 UMR 8030 - Génomique métabolique
4 AFMB - Architecture et fonction des macromolécules biologiques
5 LMGE - Laboratoire Microorganismes : Génome et Environnement
6 ICM - Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona]
7 EMBL - European Molecular Biology Laboratory [Heidelberg]
8 IBENS - Institut de biologie de l'ENS Paris
9 LOV - Laboratoire d'océanographie de Villefranche
10 SU - Sorbonne Université
11 Department of Oceanography [Honolulu]
12 MARUM - Center for Marine Environmental Sciences [Bremen]
13 PANGAEA - Data Publisher for Earth and Environmental Science
14 Bigelow Laboratory for Ocean Sciences
15 MIO - Institut méditerranéen d'océanologie
16 OSU - Ohio State University [Columbus]
17 SZN - Stazione Zoologica Anton Dohrn
18 Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
19 NSF - National Science Foundation [Arlington]
20 ADMM - Adaptation et diversité en milieu marin
21 University of Maine
22 EAPS - Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge]
23 BIOM - Biologie intégrative des organismes marins
24 Rega Institute for Medical Research [Leuven, België]
25 UCD - University College Dublin [Dublin]
26 LBDV - Laboratoire de Biologie du Développement de Villefranche sur mer
27 LMD - Laboratoire de Météorologie Dynamique (UMR 8539)
28 UBO - Université de Brest
29 DVIP Consulting
Yoann Seeleuthner
- Function : Author
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Samuel Mondy
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Vincent Lombard
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Quentin Carradec
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Eric Pelletier
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Jade Leconte
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Julie Poulain
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Karine Labadie
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Ramiro Logares
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Marcel Salanoubat
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Marc Picheral
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Chris Bowler
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Pascal Hingamp
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Matthew B. Sullivan
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Daniele Iudicone
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Ramon Massana
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Jean-Marc Aury
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Olivier Jaillon
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Colomban de Vargas
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Patrick Wincker
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Emmanuel Boss
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Gabriel Gorsky
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Fabrice Not
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Lars Stemmann
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Abstract
Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal $Tara$ Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.
Origin : Publisher files allowed on an open archive
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