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Atlantic Salmon Genome Offers Look at Rediploidization

Atlantic salmon

NEW YORK (GenomeWeb) – Members of the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG ) have published an analysis of a new, high-quality genome sequence for the Atlantic salmon, Salmo salar.

The team, made up of researchers from Canada, Norway, the US, Chile, Sweden, and China, introduced the Atlantic salmon sequencing project in a 2010 letter to Genome Biology and announced completion of the Atlantic salmon genome at a salmonid biology conference in 2014.

The new analysis, published online today in Nature, includes a look at repeat expansions, duplicate gene retention, and re-diploidization patterns in the Atlantic salmon lineage since a vertebrate whole-genome duplication specific to salmonid ancestors some 80 million years ago. It also highlights genes that have taken on new functions since this duplication through neo-functionalization, a process that appears to have occurred more frequently than sub-functionalization of ancestral gene sequences.

The researchers believe the Atlantic salmon genome assembly will serve as a resource for those attempting to come up with improved aquaculture approaches or conservation strategies for wild Atlantic salmon. The genome may also help in interpreting genetic studies of related salmonid family fish such as the rainbow trout, Oncorhynchus mykiss, as demonstrated in preliminary analyses in the current study.

"The conservation of large collinear blocks between Salmo and Oncorhynchus strongly suggests that the Atlantic salmon genome information will facilitate exploitation of genomic information in a wide range of ecological, evolutionary, conservation, and production biology settings within salmonids," senior authors William Davidson of Simon Fraser University and Stig Omholt of the Norwegian University of Science and Technology, and their colleagues, wrote.

The salmonid family contains 11 genera and 70 or more fish species, including species important to aquaculture, recreational fishing, and other industries, ICSASG researchers noted. While all bony teleost fish have undergone three different rounds of whole-genome duplication, the team noted, a fourth vertebrate genome duplication has been documented in the salmonid lineage, leading to autotetraploidization and a long, slow process of re-diploidization that may still be underway.

"Salmonids … appear to provide an unprecedented opportunity for studying vertebrate genome evolution after an autotetraploid [whole-genome duplication] over a time period that is long enough to reveal long-term evolutionary patterns, but short enough to give a high-resolution picture of the process," the authors explained.

With that in mind, the researchers used a combination of Sanger and Illumina sequencing instruments to tackle DNA from a double-haploid female Atlantic salmon individual developed through mitotic androgenesis, putting the resulting reads together into a genome assembly spanning nearly 3 billion bases. They placed some 2.24 billion bases of that sequence into salmon chromosomes.

With the help of complementary DNA, expressed sequence tag data, and transcriptome sequences for more than a dozen Atlantic salmon tissues, the team detected 37,206 high-confidence protein-coding genes, along with repeat sequences making up between 58 percent and 60 percent of the genome.

To delve into features that have contributed to re-diploidization of the Atlantic salmon genome, the researchers not only looked for clusters of duplicated salmon sequences and re-diploidization-related rearrangements, but also compared salmon gene families and genome structures with those found in related fish such as the rainbow trout.

For example, the team estimated that most duplicated genes were re-diploidized within 20 million years of the salmonid-specific whole-genome duplication event thorough large genome reorganizations that may have been partly fueled by transposable element expansions — results that differ from the slow, incremental return to diploidization described by French researchers who sequenced the rainbow trout genome in 2014.

The production of pseudogenes seemed to account for much of the post-duplication gene loss the researchers detected in the salmon genome. Among the retained genes, they did not see an over-representation of genes that stuck around after the prior vertebrate whole-genome duplication.