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The Atlantic salmon genome provides insights into rediploidization.


ABSTRACT: The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

SUBMITTER: Lien S 

PROVIDER: S-EPMC8127823 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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The Atlantic salmon genome provides insights into rediploidization.

Lien Sigbjørn S   Koop Ben F BF   Sandve Simen R SR   Miller Jason R JR   Kent Matthew P MP   Nome Torfinn T   Hvidsten Torgeir R TR   Leong Jong S JS   Minkley David R DR   Zimin Aleksey A   Grammes Fabian F   Grove Harald H   Gjuvsland Arne A   Walenz Brian B   Hermansen Russell A RA   von Schalburg Kris K   Rondeau Eric B EB   Di Genova Alex A   Samy Jeevan K A JK   Olav Vik Jon J   Vigeland Magnus D MD   Caler Lis L   Grimholt Unni U   Jentoft Sissel S   Våge Dag Inge DI   de Jong Pieter P   Moen Thomas T   Baranski Matthew M   Palti Yniv Y   Smith Douglas R DR   Yorke James A JA   Nederbragt Alexander J AJ   Tooming-Klunderud Ave A   Jakobsen Kjetill S KS   Jiang Xuanting X   Fan Dingding D   Hu Yan Y   Liberles David A DA   Vidal Rodrigo R   Iturra Patricia P   Jones Steven J M SJ   Jonassen Inge I   Maass Alejandro A   Omholt Stig W SW   Davidson William S WS  

Nature 20160418 7602


The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4  ...[more]

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