Open Access Research article

Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

Jong S Leong1, Stuart G Jantzen1, Kristian R von Schalburg1, Glenn A Cooper1, Amber M Messmer1, Nancy Y Liao2, Sarah Munro2, Richard Moore2, Robert A Holt2, Steven JM Jones2, William S Davidson3 and Ben F Koop1*

  • * Corresponding author: Ben F Koop bkoop@uvic.ca

  • † Equal contributors

Author Affiliations

1 Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada

2 Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4E6 Canada

3 Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada

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BMC Genomics 2010, 11:279  doi:10.1186/1471-2164-11-279

Published: 30 April 2010

Abstract

Background

Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution.

Results

From existing expressed sequence tag (EST) resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (Esox lucius) ESTs. Pairwise dN/dS comparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates.

Conclusions

9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate.