Homeologous regions in the Atlantic salmon genome

Eighty million years ago, a mutant fish was born that turned out to be very successful. This mutant had a double set of hereditary material – 50 chromosomes instead of the usual 25 – and it became the ancestor of all the salmonid fishes. A lot has happened during the course of this speciation and diversification: chromosomes have split up and been jumbled around, and many gene duplicates have been lost. But even today, about half of salmon genes exist in two copies, possibly linked to the ecological flexibility of salmonids. The CIGENE team have driven the sequencing of the salmon genome from its inception to its recent publication in Nature.

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.

Lien et al (2016) The Atlantic salmon genome provides insights into rediploidization. Nature 533:200-207. doi:10.1038/nature17164.

Browse the salmon genome at salmobase.org or NCBI.

Homeologous regions in the Atlantic salmon genome
The duplicated salmon genome. The figure shows salmon’s 29 chromosomes arranged in a circle. Coloured bands connect regions that have very similar DNA sequences, showing that they have been jumbled around since the whole-genome duplication. Figure 2 from Lien et al (2016), doi:10.1038/nature17164. Circos plot created by Torfinn Nome.