Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis
Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis
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DOI：
10.1093/molbev/msj051
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发表时间：
2006-02-01
影响因子：
10.7
通讯作者：
dePamphilis, CW
中科院分区：
文献类型：
--
作者：
Duarte, JM;Cui, LY;dePamphilis, CW
基因重复在多样性和新功能的进化中发挥着重要作用，并且在开花植物的核基因组中尤其普遍。重复基因可以通过表达或编码序列水平的亚功能化和新功能化来维持。为了检验重复的调控基因将以指示调控亚功能化和/或新功能化的特定方式差异表达的假设，我们检查了拟南芥中重复的调控基因的表达模式转变。对 280 个系统发育鉴定的旁系同源对的表达数据进行了双向方差分析。从野生型根、茎、叶、发育中的花序、近成熟花芽和籽荚的全局表达谱中提取表达数据。检查了基因、器官和基因与器官相互作用 (G X O) 的影响。结果表明，85% 的旁系同源对表现出显着的 G X O 效应，表明调节亚功能化和/或新功能化。在 45% 的成对比较中，显着的 G X O 效应与互补表达模式相关。没有检测到 G X O 效应和通过非同义替换与同义替换的比率检测到的放宽进化约束之间的关联。通过 II 型 MADS-box 基因系统发育推断出的祖先基因表达模式表明了调节性新功能化和器官特异性非功能化的几个案例。跨器官基因表达水平的完整连锁聚类表明每个器官的调控模块是独立的或祖先基因的表达有限。我们提出了新的分类，即调节功能低下，旁系同源对的一个成员的表达水平总体下降，同时仍然具有显着的 G X O 效应。我们得出结论，特别表明亚功能化和/或新功能化的表达差异有助于拟南芥中大多数（如果不是全部）重复调控基因的维持，并假设这导致每轮重复后调控基因的表达多样性或特异性增加。
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 it 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, stern, 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 it 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 it G X O effect and it relaxed evolutionary constraint its detected by the ratio of nonsynonymous to synonymous substitutions. Ancestral gene expression patterns inferred across it 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 it 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.