Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium.
Plant Physiol. 2011 Jul;156(3):1316-30. doi: 10.1104/pp.111.177865. Epub 2011 May 13.
Microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. We developed a robust framework to measure expression context conservation (ECC) and found, by analyzing 4,630 pairs of orthologous Arabidopsis and rice genes, that 77% showed conserved coexpression. Examples of nonconserved ECC categories suggested a link between regulatory evolution and environmental adaptations and included genes involved in signal transduction, response to different abiotic stresses, and hormone stimuli. To identify genomic features that influence expression evolution, we analyzed the relationship between ECC, tissue specificity, and protein evolution. Tissue-specific genes showed higher expression conservation compared with broadly expressed genes but were fast evolving at the protein level. No significant correlation was found between protein and expression evolution, implying that both modes of gene evolution are not strongly coupled in plants. By integration of cis-regulatory elements, many ECC conserved genes were significantly enriched for shared DNA motifs, hinting at the conservation of ancestral regulatory interactions in both model species. Surprisingly, for several tissue-specific genes, patterns of concerted network evolution were observed, unveiling conserved coexpression in the absence of conservation of tissue specificity. These findings demonstrate that orthologs inferred through sequence similarity in many cases do not share similar biological functions and highlight the importance of incorporating expression information when comparing genes across species.
微阵列实验产生了大量的表达信息，这些信息是在各种条件下对模式物种拟南芥（Arabidopsis thaliana）和水稻（Oryza sativa）进行测量得到的。将多个实验分组的表达综合库使得在一个物种内定义相关的基因表达模式并研究表达在物种之间是如何进化的成为可能。我们开发了一个强大的框架来衡量表达背景保守性（ECC），并通过分析 4630 对拟南芥和水稻的同源基因发现，77%的基因表现出保守的共表达。非保守 ECC 类别的例子表明了调控进化和环境适应之间的联系，包括参与信号转导、对不同非生物胁迫和激素刺激的反应的基因。为了识别影响表达进化的基因组特征，我们分析了 ECC、组织特异性和蛋白质进化之间的关系。与广泛表达的基因相比，组织特异性基因表现出更高的表达保守性，但在蛋白质水平上进化得更快。没有发现 ECC 和蛋白质进化之间有显著的相关性，这意味着在植物中，这两种基因进化模式没有紧密结合。通过顺式调控元件的整合，许多 ECC 保守基因显著富集了共享的 DNA 基序，暗示在这两个模式物种中，祖先调控相互作用的保守。令人惊讶的是，对于几个组织特异性基因，观察到协同网络进化的模式，揭示了在没有组织特异性保守的情况下保守的共表达。这些发现表明，通过序列相似性推断的同源基因在许多情况下并不具有相似的生物学功能，并强调了在比较物种间基因时纳入表达信息的重要性。
