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DNA Res. 2018 Feb 21. doi: 10.1093/dnares/dsy005. [Epub ahead of print]

Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis.

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Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan.
CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.
Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
Center of Ecological Research, Kyoto University, Hirano, Otsu, Shiga 520-2113, Japan.
Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan.
College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan.


Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae. The duplication frequency of retained genes in the Arabidopsis lineage was ∼10 times higher than the duplication frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss (Physcomitrella patens). The difference of duplication frequencies can be explained by a rapid decay of anciently duplicated genes. To examine the degree of selection pressure on genes duplicated in either the A. halleri-lyrata or the A. halleri lineage, we examined positive and purifying selection in the A. halleri-lyrata and A. halleri lineages throughout the ratios of nonsynonymous to synonymous substitution rates (KA/KS). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. Interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication compared with immediately after gene duplication.

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