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A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum

文献类型：期刊论文

作者Rastogi, Achal2,7; Vieira, Fabio Rocha Jimenez2; Deton-Cabanillas, Anne-Flore2; Veluchamy, Alaguraj1,2; Cantrel, Catherine2; Wang, Gaohong3; Vanormelingen, Pieter4; Bowler, Chris2; Piganeau, Gwenael5; Hu, Hanhua3
刊名ISME JOURNAL
出版日期2020-02-01
卷号14期号:2页码:347-363
ISSN号1751-7362
DOI10.1038/s41396-019-0528-3
通讯作者Hu, Hanhua(hanhuahu@ihb.ac.cn) ; Tirichine, Leila(tirichine-l@univ-nantes.fr)
英文摘要Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.
WOS关键词POPULATION GENOMICS ; SEXUAL REPRODUCTION ; CRYPTIC SPECIATION ; PROTEIN FAMILY ; METHYLATION ; EVOLUTION ; SELECTION ; LIGHT ; TOOL ; PHYTOPLANKTON
资助项目National Natural Science Foundation of China[91751117] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA17010502] ; ERC Advanced Award 'Diatomite' ; LouisD Foundation of the Institut de France ; Gordon and Betty Moore Foundation ; French Government 'Investissements d'Avenir' program MEMO LIFE[ANR-10-LABX-54] ; French Government 'Investissements d'Avenir' program PSL* Research University[ANR-1253 11-IDEX-0001-02] ; French Government 'Investissements d'Avenir' program OCEANOMICS[ANR11-BTBR-0008] ; Radcliffe Institute of Advanced Study at Harvard University ; MEMO LIFE[ANR-10-LABX-54] ; region of Pays de la Loire (ConnecTalent EPIALG project) ; International PhD fellowship from MEMO LIFE[ANR-10-LABX-54] ; CNRS
WOS研究方向Environmental Sciences & Ecology ; Microbiology
语种英语
WOS记录号WOS:000509197100003
出版者NATURE PUBLISHING GROUP
资助机构National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; CNRS ; CNRS ; CNRS ; CNRS ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; CNRS ; CNRS ; CNRS ; CNRS ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; CNRS ; CNRS ; CNRS ; CNRS ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Strategic Priority Research Program of the Chinese Academy of Sciences ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; ERC Advanced Award 'Diatomite' ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; LouisD Foundation of the Institut de France ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; Gordon and Betty Moore Foundation ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program MEMO LIFE ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program PSL* Research University ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; French Government 'Investissements d'Avenir' program OCEANOMICS ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; Radcliffe Institute of Advanced Study at Harvard University ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; MEMO LIFE ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; region of Pays de la Loire (ConnecTalent EPIALG project) ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; International PhD fellowship from MEMO LIFE ; CNRS ; CNRS ; CNRS ; CNRS
源URL[http://ir.ihb.ac.cn/handle/342005/35437]  
专题水生生物研究所_藻类生物学及应用研究中心_期刊论文
通讯作者Hu, Hanhua; Tirichine, Leila
作者单位1.King Abdullah Univ Sci & Technol, Ctr Desert Agr, Biol & Environm Sci & Engn Div, Thuwal 239556900, Saudi Arabia
2.PSL Univ Paris, IBENS, INSERM, CNRS,Ecole Normale Super, F-75005 Paris, France
3.Chinese Acad Sci, Inst Hydrobiol, Key Lab Algal Biol, Wuhan 430072, Peoples R China
4.Univ Ghent, Dept Biol, Res Grp Protistol & Aquat Ecol, Krijgslaan 281-S8, B-9000 Ghent, Belgium
5.UPMC Univ Paris 06, Sorbonne Univ, CNRS, BIOM,Observ Oceanol, F-66650 Banyuls Sur Mer, France
6.Univ Nantes, CNRS, UFIP, UMR 6286, F-44000 Nantes, France
7.Corteva Agrisci TM, Atria Block,12th Floor, Hyderabad 500081, Andhra Pradesh, India
推荐引用方式
GB/T 7714		 Rastogi, Achal,Vieira, Fabio Rocha Jimenez,Deton-Cabanillas, Anne-Flore,et al. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum[J]. ISME JOURNAL,2020,14(2):347-363.
APA Rastogi, Achal.,Vieira, Fabio Rocha Jimenez.,Deton-Cabanillas, Anne-Flore.,Veluchamy, Alaguraj.,Cantrel, Catherine.,...&Tirichine, Leila.(2020).A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum.ISME JOURNAL,14(2),347-363.
MLA Rastogi, Achal,et al."A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum".ISME JOURNAL 14.2(2020):347-363.

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来源：水生生物研究所

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