Journal Article

Locally Duplicated Ohnologs Evolve Faster Than Nonlocally Duplicated Ohnologs in <i>Arabidopsis</i> and Rice

Yupeng Wang

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 5, issue 2, pages 362-369
Published in print January 2013 |
Published online January 2013 | e-ISSN: 1759-6653 | DOI: https://dx.doi.org/10.1093/gbe/evt016

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Whole-genome duplications (WGDs) have recurred in the evolution of angiosperms, resulting in many duplicated chromosomal segments. Local gene duplications are also widespread in angiosperms. WGD-derived duplicates, that is, ohnologs, and local duplicates often show contrasting patterns of gene retention and evolution. However, many genes in angiosperms underwent multiple gene duplication events, possibly by different modes, indicating that different modes of gene duplication are not mutually exclusive. In two representative angiosperm genomes, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), we found that 9.6% and 11.3% of unique ohnologs, corresponding to 15.5% and 17.1% of ohnolog pairs, were also involved in local duplications, respectively. Locally duplicated ohnologs are widely distributed in different duplicated chromosomal segments and functionally biased. Coding sequence divergence between duplicated genes is denoted by nonsynonymous (Ka) and synonymous (Ks) substitution rates. Locally duplicated ohnolog pairs tend to have higher Ka, Ka/Ks, and gene expression divergence than nonlocally duplicated ohnolog pairs. Locally duplicated ohnologs also tend to have higher interspecies sequence divergence. These observations indicate that locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs. This study highlights the necessity to take local duplications into account when analyzing the evolutionary dynamics of ohnologs.

Keywords: local gene duplication; whole-genome duplication; ohnolog; divergence; colinearity

Journal Article.  3403 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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