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

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Kousuke HanadaShin-Ichi Morinaga

Abstract

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....Continue Reading

Citations

Aug 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·K H WolfeW H Li
Jul 10, 1997·Nature·M A NowakJ M Smith
Nov 10, 2000·Science·M Lynch, J S Conery
Dec 29, 2000·Nature·Arabidopsis Genome Initiative
Dec 18, 2001·Journal of Molecular Biology·M RemmE L Sonnhammer
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Apr 8, 2003·Molecular Biology and Evolution·Jing YangWen-Hsiung Li
Mar 17, 2004·PLoS Biology·Jerel C Davis, Dmitri A Petrov
Jul 9, 2004·BMC Evolutionary Biology·I King JordanEugene V Koonin
Jul 15, 2004·PLoS Biology·Andrew FortnaJames M Sikela
Nov 13, 2004·Molecular Biology and Evolution·M Mar Albà, Jose Castresana
Nov 20, 2004·Science·Li-Zhi Gao, Hideki Innan
Dec 15, 2004·Annals of Botany·J Spencer JohnstonH James Price
Feb 1, 2005·Trends in Genetics : TIG·Steven Lockton, Brandon S Gaut
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Jun 16, 2005·Plant Physiology·Kentaro K Shimizu, Michael D Purugganan
Jun 18, 2005·Genome Biology·Nils RostoksRobbie Waugh
Sep 5, 2006·PLoS Computational Biology·Carene RizzonBrandon S Gaut
Mar 27, 2007·Trends in Genetics : TIG·Deyou Zheng, Mark B Gerstein
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
May 9, 2007·Nucleic Acids Research·Andreas UntergasserJack A M Leunissen
Apr 23, 2008·Current Protocols in Bioinformatics·James C Wilgenbusch, David Swofford
Nov 19, 2008·Nature Reviews. Genetics·Gavin C Conant, Kenneth H Wolfe
Feb 5, 2009·The New Phytologist·Nathalie VerbruggenHenk Schat
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Apr 9, 2009·Proceedings of the National Academy of Sciences of the United States of America·Yuri I WolfDavid J Lipman
Jul 31, 2009·Plant Physiology·Cheng ZouShin-Han Shiu
Jan 27, 2010·Nature Genetics·Thomas L TurnerSergey V Nuzhdin
Mar 3, 2010·Annual Review of Plant Biology·Ute Krämer
Jan 1, 2009·Genome Biology and Evolution·Kousuke HanadaKazuo Shinozaki
May 4, 2010·BMC Evolutionary Biology·Andrew S WarrenLiqing Zhang
Aug 26, 2010·Molecular Biology and Evolution·Kousuke HanadaMasami Yokota Hirai
Oct 6, 2010·Genome Research·Anchal VishnoiJoshua B Plotkin
Oct 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Mark A BeilsteinSarah Mathews
Mar 11, 2011·Molecular Biology and Evolution·Liang Yang, Brandon S Gaut
Jul 9, 2011·Science·Timothy M Heckman, Guinevere Kauffmann

Related Concepts

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