Complex Genes Are Preferentially Retained After Whole-Genome Duplication in Teleost Fish

Abstract

Gene duplication generates new genetic material which, if retained after duplication, may contribute to organismal evolution. A whole-genome duplication occurred in the ancestry of teleost fish and consequently there are many duplicated genes in teleost genomes. Indeed, it has been proposed that the evolutionary diversification of teleost fish may have been stimulated by the fish-specific genome duplication (FSGD). However, it is not clear which factors determine which genes are retained as duplicate copies and which return to a singleton state after duplication. In the present study, gene complexity, in terms of encoded protein length and functional domain number, is compared between duplicate and singleton genes for nine well-annotated teleost genomes. A total of 933 gene families with retained duplicates and 4590 singleton gene families are analysed. Genes with retained duplicates are found to be significantly longer (27.9–38.2%) and to have more functional domains (20.5–26.5%) than singleton genes in all the nine teleost genomes, suggesting that genes encoded longer proteins with and more functional domains were preferentially retained after whole-genome duplication in teleosts. This differential retention of duplicated genes will have increased the genomic complexity of teleost fish after FSGD which, together with differential duplicated gene retention as a lineage-splitting force, may have greatly contributed to the successful diversification of teleost fish.