Publication Date:
2012-06-16
Description:
Background: Gene duplication has had a major impact on genome evolution. Localized (or tandem)duplication resulting from unequal crossing over and whole genome duplication are believedto be the two dominant mechanisms contributing to vertebrate genome evolution. Whilemuch scrutiny has been directed toward discerning patterns indicative of whole-genomeduplication events in teleost species, less attention has been paid to the continuous nature ofgene duplications and their impact on the size, gene content, functional diversity, and overallarchitecture of teleost genomes. Results: Here, using a Markov clustering algorithm directed approach we catalogue and analyzepatterns of gene duplication in the four model teleost species with chromosomal coordinates: zebrafish, medaka, stickleback, and Tetraodon. Our analyses based on set size, duplicationtype, synonymous substitution rate (Ks), and gene ontology emphasize shared and lineagespecificpatterns of genome evolution via gene duplication. Most strikingly, our analyseshighlight the extraordinary duplication and retention rate of recent duplicates in zebrafish andtheir likely role in the structural and functional expansion of the zebrafish genome. We findthat the zebrafish genome is remarkable in its large number of duplicated genes, smallduplicate set size, biased Ks distribution toward minimal mutational divergence, andproportion of tandem and intra-chromosomal duplicates when compared with the otherteleost model genomes. The observed gene duplication patterns have played significant rolesin shaping the architecture of teleost genomes and appear to have contributed to the recentfunctional diversification and divergence of important physiological processes in zebrafish. Conclusions: We have analyzed gene duplication patterns and duplication types among the available teleostgenomes and found that a large number of genes were tandemly and intrachromosomallyduplicated, suggesting their origin of independent and continuous duplication. This isparticularly true for the zebrafish genome. Further analysis of the duplicated gene setsindicated that a significant portion of duplicated genes in the zebrafish genome were ofrecent, lineage-specific duplication events. Most strikingly, a subset of duplicated genes isenriched among the recently duplicated genes involved in immune or sensory responsepathways. Such findings demonstrated the significance of continuous gene duplication aswell as that of whole genome duplication in the course of genome evolution.
Electronic ISSN:
1471-2164
Topics:
Biology
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