The Atlantic salmon genome provides insights into rediploidization

Authors: LIEN, SIGBORN - Centre For Integrative Genetics (CIGENE); KOOP, BEN - University Of Victoria; SANDVE, SIMEN - Centre For Integrative Genetics (CIGENE); MILLER, JASON - J Craig Venter Institute; KENT, MATTHEW - Centre For Integrative Genetics (CIGENE); NOME, TORFINN - Centre For Integrative Genetics (CIGENE); HVIDSTEN, TORGEIR - Norwegian University Of Life Sciences; LEONG, JONG - University Of Victoria; MINKLEY, DAVID - University Of Victoria; GRAMMES, FABIAN - Centre For Integrative Genetics (CIGENE); GROVE, HAROLD - Centre For Integrative Genetics (CIGENE); GJUVSLAND, ARNE - Centre For Integrative Genetics (CIGENE); KARLOSS, JEEVAN - Centre For Integrative Genetics (CIGENE); VAGE, DAG INGE - Centre For Integrative Genetics (CIGENE); VIK, JON OLAV - Centre For Integrative Genetics (CIGENE); VIGELAND, MAGNUS - University Of Oslo; VON SCHALBURG, KRIS - University Of Victoria; RONDEAU, ERIC - University Of Victoria; DI GENOVA, ALEX - Adolfo Ibanez University; GRIMHOLT, UNNI - Norwegian Veterinary Institute; JENTOFT, SISSEL - University Of Oslo; DE JONG, PIETER - Children'S Hospital Oakland Research Institute; MOEN, THOMAS - Aquagen; BARANSKI, MATHTHEW - Nofima; Palti, Yniv; ZIMIN, ALEKSEY - University Of Maryland; WALENZ, BRIAN - J Craig Venter Institute; NEDERBRAGT, LEX - University Of Oslo; LIBERLES, DAVID - University Of Wyoming; VIDAL, RODRIGO - University Of Santiago; ITURRA, PATRICIA - Universidad De Chile; JONES, STEVEN J.M. - Genome Science Centre-Canada; OMHOLT, STIG - Norwegian University; DAVIDSON, WILLIAM - Simon Frasier University

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2016
Publication Date: 5/12/2016
Publication URL: http://handle.nal.usda.gov/10113/62850
Citation: Palti, Y., Lien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Nome, T., Hvidsten, T.R., Leong, J., Minkley, D., Grammes, F., Grove, H., Gjuvsland, A., Karloss, J., Iturra, P., Jones, S., Omholt, S.W., Davidson, W.S., Kent, M.P. 2016. The Atlantic salmon genome provides insights into rediploidization. Nature. 533: 200-2012. doi:10.1038/nature17164.

Interpretive Summary: A genome physical map of an organism is composed of the organism's chromosomes and the unique sequence of DNA bases along each chromosome. Genome assembly is a process in which a large number of short DNA sequences are put together in a continuous tandem to represent the original chromosome until the genome map of all the chromosomes is completed. The information from genome assembly of an organism is used by scientists to attach biological information to the blueprint of the living organism. The completion of the human genome over a decade ago was one of the most important landmarks in modern science and the abundance of biological information extracted from it has led to breakthrough discoveries in medical research with enormous impact on all life science research. Similarly, the bovine genome assembly has led to breakthrough discoveries in agricultural research and the development of new genome-enabled strategies for animal breeding. In the current report the genome assembly of Atlantic salmon, one of the most economically important fish species, is described including analyses that shed light on the evolution of all salmonids. Part of the analysis involves comparing between the Atlantic salmon genome and the incomplete assembly of the rainbow trout genome and showing that the salmon assembly can be used as a good reference for the genome of other salmonids. Like other agricultural animals and plants, it is expected that the new high quality genome assembly will provide the needed information for high impact biological research with potential for spurring major scientific discoveries and many new developments in fish farming and breeding.

Technical Abstract: The common ancestor of salmonids underwent an autotetraploid whole genome duplication event (Ss4R) approximately eighty million years ago, which provides unique opportunities to study the early evolutionary fate of a duplicated vertebrate genome in different extant lineages. Here, we present a high quality genome assembly for Atlantic salmon genome and demonstrate that it can serve as a reference sequence for other salmonids for a range of purposes. We show that large genomic reorganizations, coinciding with a burst of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. By comparing salmon duplicate gene expression patterns across a wide range of tissues with those of orthologous genes in a fish outgroup species representing the pre-Ss4R state, we demonstrate that the number of instances of neofunctionalization greatly exceeds the number of subfunctionalization cases. Through use of existing gene family data for all teleosts providing information about gene duplicate retention after the teleost-specific whole genome duplication 320 MYA, we show that post-Ss4R nonfunctionalization of duplicates appears to be a stochastic process without particular enrichment of specific genes.