Selection-Driven Divergence After Gene Duplication in Arabidopsis thaliana
Selection-Driven Divergence After Gene Duplication in Arabidopsis thaliana
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DOI：
10.1007/s00239-011-9463-2
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发表时间：
2011-10-01
影响因子：
3.9
通讯作者：
Schmid, Karl J.
中科院分区：
文献类型：
--
作者：
Gossmann, Toni I.;Schmid, Karl J.
基因复制是进化新奇性起源的最重要机制之一。尽管复制基因的命运的各种模型已经建立，目前的知识，基因复制后的分歧选择的作用是相当有限的。在这项研究中，我们分析了序列分歧，响应新的和亚功能化的片段重复基因在拟南芥基因组中。我们比较了A. thaliana和白杨Populus duccarpa的同源序列，以鉴定基因的正向同源对及其相应的旁系同源物。A.对非同义和同义替换率比（ω = d（N）/d（S））的最大似然分析。使用拟南芥旁系同源物检测蛋白质编码序列进化速率的差异。我们分析了1，924 A。thaliana旁系同源对，我们的结果表明，大约6.9%的位点的一小部分显示出谱系之间的Ω值不同。我们观察到调控序列的富集、共表达水平的降低和取代数量的增加，这可以归因于基于McDonald-Kreitman类型分析的正选择。总之，这些结果表明，重复后的选择大大有助于基因的新颖性，因此在植物中的功能分歧。
Gene duplications are one of the most important mechanisms for the origin of evolutionary novelties. Even though various models of the fate of duplicated genes have been established, current knowledge about the role of divergent selection after gene duplication is rather limited. In this study, we analyzed sequence divergence in response to neo- and subfunctionalization of segmentally duplicated genes in the genome of Arabidopsis thaliana. We compared the genomes of A. thaliana and the poplar Populus trichocarpa to identify orthologous pairs of genes and their corresponding inparalogs. Maximum-likelihood analyses of the nonsynonymous and synonymous substitution rate ratio (omega = d(N)/d(S))of pairs of A. thaliana inparalogs were used to detect differences in the evolutionary rates of protein coding sequences. We analyzed 1,924 A. thaliana paralogous pairs and our results indicate that around 6.9% show divergent omega values between the lineages for a fraction of sites. We observe an enrichment of regulatory sequences, a reduced level of co-expression and an increased number of substitutions that can be attributed to positive selection based on an McDonald-Kreitman type of analysis. Taken together, these results show that selection after duplication contributes substantially to gene novelties and hence functional divergence in plants.