The Atlantic salmon genome provides insights into rediploidization
2016 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 533, no 7602, 200-205 p.Article in journal (Refereed) PublishedText
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.
Place, publisher, year, edition, pages
Nature Publishing Group, 2016. Vol. 533, no 7602, 200-205 p.
IdentifiersURN: urn:nbn:se:umu:diva-121444DOI: 10.1038/nature17164ISI: 000376007200040PubMedID: 27088604OAI: oai:DiVA.org:umu-121444DiVA: diva2:941322