Mol Biol Evol:中科院植物所葛颂研究组发表植物生态式物种形成研
9月10日molecular Biology and Evolution 期刊上在线发表中国科学院植物研究所葛颂研究组的一项研究结果。葛颂研究组助理研究员郭洁为论文的第一作者。
生态式物种形成是新物种产生的重要方式。尽管已有大量研究探索其遗传机理，但对表达调控在生态式物种形成中的作用仍知之甚少。近日，中国科学院植物研究所葛颂研究组以野生稻为材料，在全基因组水平上探讨了表达调控进化在物种形成和适应性进化中的作用。
栽培稻近缘野生种Oryza rufipogon 和O. nivara 是近期分化的姊妹种，在形态、生境和生殖等方面存在显著差异，因此是研究物种形成的理想体系。研究人员通过对2个野生种3个生殖相关组织的转录组进行测序，发现约8%的基因在种间发生了显著的表达分化，并随机分布在基因组上。其中，约62%差异表达基因的表达模式受方向性选择的影响;相对于编码区，差异表达基因上游区域比非差异表达基因进化速度更快，说明基因调控在物种分化中起到了关键作用。进一步功能注释分析发现，差异表达基因显著集中在与生殖和逆境响应相关的基因上，这与2个野生种在表型和生态上的分化相一致。
该研究首次在全基因组水平上探讨了基因调控在植物物种形成中的作用，说明生态式物种形成伴随着广泛且具有适应性的表达分化，为进一步理解植物物种形成提供了重要证据。
基因组表达分化分布模式(a和b图为差异表达和方向性选择基因的韦恩图;c图为差异表达基因在基因组上的分布情况。不同颜色代表不同组织)
原文链接：
Widespread and Adaptive Alterations in Genome-Wide Gene expression Associated with Ecological Divergence of Two Oryza Species
原文摘要：
Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression technology and the paired-end RNA sequencing method, we obtained 21,415 expressed genes across three reproduction-related tissues. Of them, approximately 8% (1,717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1,064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5′ flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and provide new insights into the importance of regulatory evolution in ecological speciation in plants.
作者：葛颂
