MBE Advance Access published online on November 9, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj051
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1 Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
* To whom correspondence should be addressed. Gene duplication plays an important role in the evolution of diversity and novel function and is especially prevalent in the nuclear genomes of flowering plants. Duplicate genes may be maintained through sub- and neofunctionalization at the level of expression or coding sequence. In order to test the hypothesis that duplicated regulatory genes will be differentially expressed in a specific manner indicative of regulatory subfunctionalization and/or neofunctionalization, we examined expression pattern shifts in duplicated regulatory genes in Arabidopsis. A two-way analysis of variance (ANOVA) was performed on expression data for 280 phylogenetically-identified paralogous pairs. Expression data were extracted from global expression profiles for wild-type root, stem, leaf, developing inflorescence, nearly mature flowerbuds, and seed pod. Gene [G], organ [O], and gene by organ interaction [GxO] effects were examined. Results indicate that 85% of the paralogous pairs exhibited a significant GxO effect indicative of regulatory subfunctionalization and/or neofunctionalization. A significant GxO effect was associated with complementary expression patterns in 45% of pair-wise comparisons. No association was detected between a GxO effect and relaxed evolutionary constraint as detected by the ratio of nonsynonymous to synonymous substitutions. Ancestral gene expression patterns inferred across a Type II MADS box gene phylogeny suggest several cases of regulatory neofunctionalization and organ-specific nonfunctionalization. Complete linkage clustering of gene expression levels across organs suggests that regulatory modules for each organ are independent or ancestral genes had limited expression. We propose a new classification, regulatory hypofunctionalization, for an overall decrease in expression level in one member of a paralogous pair while still having a significant GxO effect. We conclude that expression divergence specifically indicative of subfunctionalization and/or neofunctionalization contributes to the maintenance of most if not all duplicated regulatory genes in Arabidopsis and hypothesize that this results in increasing expression diversity or specificity of regulatory genes after each round of duplication.
Accepted November 2, 2005
Research Article
Expression Pattern Shifts Following Duplication Indicative of Subfunctionalization and Neofunctionalization in Regulatory Genes of Arabidopsis
2 Bioinformatics Consulting Center, The Pennsylvania State University, University Park, PA 16802
3 Bioinformatics Consulting Center, The Pennsylvania State University, University Park, PA 16802; Department of Statistics, The Pennsylvania State University, University Park, PA 16802
Claude W. dePamphilis, E-mail: cwd3{at}psu.edu
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