The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

被引：715

作者：

Berthelot, Camille ^{[1
,2
,3
,4
,5
]}

Brunet, Frederic ^{[6
]}

Chalopin, Domitille ^{[6
]}

Juanchich, Amelie ^{[7
]}

Bernard, Maria ^{[4
,8
]}

Noel, Benjamin ^{[4
]}

Bento, Pascal ^{[4
]}

Da Silva, Corinne ^{[4
]}

Labadie, Karine ^{[4
]}

Alberti, Adriana ^{[4
]}

Aury, Jean-Marc ^{[4
]}

Louis, Alexandra ^{[1
,2
,3
]}

Dehais, Patrice ^{[9
]}

Bardou, Philippe ^{[9
]}

Montfort, Jerome ^{[7
]}

Klopp, Christophe ^{[9
]}

Cabau, Cedric ^{[9
]}

Gaspin, Christine ^{[10
,11
]}

Thorgaard, Gary H. ^{[12
]}

Boussaha, Mekki ^{[8
]}

Quillet, Edwige ^{[8
]}

Guyomard, Rene ^{[8
]}

Galiana, Delphine ^{[6
]}

Bobe, Julien ^{[7
]}

Volff, Jean-Nicolas ^{[6
]}

Genet, Carine ^{[8
]}

Wincker, Patrick ^{[4
,13
,14
]}

Jaillon, Olivier ^{[4
,13
,14
]}

Roest Crollius, Hugues ^{[1
,2
,3
]}

Guiguen, Yann ^{[7
]}

机构：

[1] Ecole Normale Super, Inst Biol, IBENS, F-75005 Paris, France

[2] INSERM, U1024, F-75005 Paris, France

[3] CNRS, UMR 8197, F-75005 Paris, France

[4] CEA, Inst Genom, Ctr Natl Sequencage, F-91057 Evry, France

[5] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England

[6] Ecole Normale Super Lyon, CNRS UMR UCBL 5242, Inst Genom Fonct Lyon, F-69364 Lyon 07, France

[7] INRA, Fish Physiol & Genom UR1037, F-35000 Rennes, France

[8] INRA, UMR Genet Anim & Biol Integrat 1313, F-78350 Jouy En Josas, France

[9] INRA, SIGENAE, UR 875, INRA Auzeville, F-31326 Castanet Tolosan, France

[10] INRA, UBIA UR 875, F-31320 Castanet Tolosan, France

[11] INRA, UR 875, F-31320 Castanet Tolosan, France

[12] Washington State Univ, Sch Biol Sci, Pullman, WA 99164 USA

[13] Univ Evry, UMR 8030, Evry, France

[14] CNRS, UMR 8030, Evry, France

来源：

NATURE COMMUNICATIONS | 2014年 / 5卷

关键词：

MULTIPLE SEQUENCE ALIGNMENT; INTEGRATED MAP; GENE; GENERATION; PROGRAM; SYNTENY; TIME; DIVERSIFICATION; COMPLEXITY; FAMILIES;

D O I：

10.1038/ncomms4657

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.

引用

页数：10

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