Duarte Jill M, Cui Liying, Wall P Kerr, Zhang Qing, Zhang Xiaohong, Leebens-Mack Jim, Ma Hong, Altman Naomi, dePamphilis Claude W
Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of the Life Sciences, The Pennsylvania State University, USA.
Mol Biol Evol. 2006 Feb;23(2):469-78. doi: 10.1093/molbev/msj051. Epub 2005 Nov 9.
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 subfunctionalization 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 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 flower buds, and seedpod. Gene, organ, and gene by organ interaction (G x O) effects were examined. Results indicate that 85% of the paralogous pairs exhibited a significant G x O effect indicative of regulatory subfunctionalization and/or neofunctionalization. A significant G x O effect was associated with complementary expression patterns in 45% of pairwise comparisons. No association was detected between a G x O effect and a 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 G x O 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.
基因复制在多样性和新功能的进化中起着重要作用，在开花植物的核基因组中尤为普遍。复制基因可通过表达水平或编码序列层面的亚功能化和新功能化得以保留。为了验证复制的调控基因会以特定方式差异表达这一假说，该方式表明了调控亚功能化和/或新功能化，我们研究了拟南芥中复制的调控基因的表达模式变化。对280个系统发育鉴定的旁系同源基因对的表达数据进行了双向方差分析。表达数据从野生型根、茎、叶、发育中的花序、接近成熟的花芽和豆荚的全局表达谱中提取。研究了基因、器官以及基因与器官的相互作用（G×O）效应。结果表明，85%的旁系同源基因对表现出显著的G×O效应，表明存在调控亚功能化和/或新功能化。在45%的成对比较中，显著的G×O效应与互补表达模式相关。未检测到G×O效应与非同义替换与同义替换比率所检测到的松弛进化约束之间存在关联。通过II型MADS盒基因系统发育推断出的祖先基因表达模式表明了几个调控新功能化和器官特异性无功能化的案例。跨器官的基因表达水平的完全连锁聚类表明，每个器官的调控模块是独立的，或者祖先基因的表达有限。我们提出了一种新的分类，即调控功能减退，用于描述旁系同源基因对中一个成员的表达水平总体下降，同时仍具有显著的G×O效应的情况。我们得出结论，特异性表明亚功能化和/或新功能化的表达差异有助于维持拟南芥中大多数（如果不是全部）复制的调控基因，并推测这会导致每一轮复制后调控基因的表达多样性或特异性增加。
