The Atlantic Salmon Genome Provides Insights Into Rediploidization

Nature. 2016 May 12;533(7602):200-5. doi: 10.1038/nature17164. Epub 2016 Apr 18.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • DNA Transposable Elements / genetics
  • Diploidy*
  • Evolution, Molecular*
  • Female
  • Gene Duplication / genetics*
  • Genes, Duplicate / genetics*
  • Genome / genetics*
  • Genomics
  • Male
  • Models, Genetic
  • Mutagenesis / genetics
  • Phylogeny
  • Reference Standards
  • Salmo salar / classification
  • Salmo salar / genetics*
  • Sequence Homology

Substances

  • DNA Transposable Elements