Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
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DOI：
10.1101/gr.146233.112
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发表时间：
2013-06-01
期刊：
影响因子：
7
通讯作者：
Regev, Aviv
中科院分区：
文献类型：
--
作者：
Roy, Sushmita;Wapinski, Ilan;Regev, Aviv
比较功能基因组学通过分析跨物种的功能数据（例如基因表达谱）来研究生物过程的进化。一个主要的挑战是比较在复杂的系统发育中收集的概况。在这里，我们提出了 Arboretum，一种新颖的可扩展计算算法，它将多个物种的表达数据与物种和基因系统发育相结合，以推断现有物种中共表达基因的模块及其进化历史。我们还开发了新的、普遍适用的基因调控模块的保护和分歧措施，以评估基因内容和表达的变化对模块进化的影响。我们利用植物园研究了八种子囊菌真菌对热休克的转录反应的进化，并重建了祖先环境应激反应（ESR）的模块。我们发现跨物种的应激反应以及祖先 ESR 模块的重建组件具有显着的保守性。最大的差异在于最大的诱发应力，主要是通过模块膨胀。热应激反应的差异超过了同一物种对葡萄糖消耗的反应中观察到的差异。植物园及其相关分析提供了一个全面的框架来系统地研究特定条件反应的调节演变。
Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories. We also develop new, generally applicable measures of conservation and divergence in gene regulatory modules to assess the impact of changes in gene content and expression on module evolution. We used Arboretum to study the evolution of the transcriptional response to heat shock in eight species of Ascomycota fungi and to reconstruct modules of the ancestral environmental stress response (ESR). We found substantial conservation in the stress response across species and in the reconstructed components of the ancestral ESR modules. The greatest divergence was in the most induced stress, primarily through module expansion. The divergence of the heat stress response exceeds that observed in the response to glucose depletion in the same species. Arboretum and its associated analyses provide a comprehensive framework to systematically study regulatory evolution of condition-specific responses.