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

• Published in: BMC Genomics
• Main Authors: Holt Robert A, Moore Richard, Munro Sarah, Liao Nancy Y, Messmer Amber M, Cooper Glenn A, von Schalburg Kristian R, Jantzen Stuart G, Leong Jong S, Jones Steven JM, Davidson William S, Koop Ben F
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2010
• Subjects: Biotechnology; TP248.13-248.65; Genetics; QH426-470; Atlantic salmon; Salmo salar
• Online Access: https://doi.org/10.1186/1471-2164-11-279; https://doaj.org/article/08779e0193c443b9aaa329a1e88b9a87

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 d N /d S 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.