ArticleMolecular genetics and genomics : MGG2009
Expression diversity and evolutionary dynamics of rice duplicate genes.
Article in Molecular genetics and genomics : MGG, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- Comparative and Expression Analysis of Ubiquitin Conjugating Domain-Containing Genes in TwoCells · 2018Article
- Genome Wide Identification, Evolutionary, and Expression Analysis of VQ Genes from Two Pyrus Species.Genes · 2018Article
- Genome-Wide Identification, Classification, and Expression Divergence of Glutathione-Transferase Family inBioMed research international · 2018Article
- Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean.BMC plant biology · 2016Article
- Evolutionary history of trihelix family and their functional diversification.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- PLANEX: the plant co-expression database.BMC plant biology · 2013Article
- Genome-wide identification, characterization and expression analysis of populus leucine-rich repeat receptor-like protein kinase genes.BMC genomics · 2013Article
- Insight into the molecular evolution of non-specific lipid transfer proteins via comparative analysis between rice and sorghum.DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
- Molecular sequence variations of the lipoxygenase-2 gene in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- Comparative analysis of evolutionary dynamics of genes encoding leucine-rich repeat receptor-like kinase between rice and Arabidopsis.Genetica · 2011Article
- ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs.BMC plant biology · 2011Article
- A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes.Plant molecular biology · 2010Article
- Extensive functional diversification of the Populus glutathione S-transferase supergene family.The Plant cell · 2009Article
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3 authors.
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Abstract
Duplicate genes are believed to be a major source of new gene functions over evolutionary time. In order to evaluate the evolutionary dynamics of rice duplicate genes, formed principally by paleoployploidization prior to the speciation of the Poaceae family, we have employed a public microarray dataset including 155 gene expression omnibus sample plates and bioinformatics tools. At least 57.4% of old approximately 70 million years ago (MYA) duplicate gene pairs exhibit divergences in expression over the given experimental set, whereas at least 50.9% of young approximately 7.7-MYA duplicate gene pairs were shown to be divergent. When grouping the rice duplicate genes according to functional categories, we noted a striking and significant enrichment of divergent duplicate metabolism-associated genes, as compared to that observed in non-divergent duplicate genes. While both non-synonymous substitution (Ka) and synonymous substitution (Ks) values between non- and divergent duplicate gene pairs evidenced significant differences, the Ka/Ks values between them exhibited no significant differences. Interestingly, the average numbers of conserved motifs of the duplicate gene pairs revealed a pattern of decline along with an increase in expression diversity, partially supporting the subfunctionalization model with degenerative complementation in regulatory motifs. Duplicate gene pairs with high local similarity (HLS) segments, which might be formed via conversion between rice paleologs, evidenced higher expression correlations than were observed in the gene pairs without the HLS segments; this probably resulted in an increased likelihood of gene conversion in promoters of the gene pairs harboring HLS segments. More than 30% [corrected] of the rice gene families exhibited similar high expression diversity between members as compared to that of randomly selected gene pairs. These findings are likely reflective of the evolutionary dynamics of rice duplicate genes for gene retention.
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