Comparative proteome analysis across moss, monocots and dicots unveils the evolutionary dynamics of core processes

Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here we present a novel multi-species proteomic dataset and a computational pipeline to compare the protein levels across multiple plant species systematically. Globally we find that protein levels diverge according to phylogenetic distance, but is more constrained than at the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the important role of autophagy and redox management processes in this symbiotic association.

比较功能基因组学（Comparative functional genomics）是研究物种演化的有力手段。迄今为止，此类研究大多聚焦于哺乳动物与酵母系统发育中的转录组（transcriptome）。本研究公开了一套全新的多物种蛋白质组学（proteomic）数据集与一套计算分析流程，可系统性比对多种植物物种间的蛋白质表达水平。整体分析显示，蛋白质表达水平随系统发育距离发生分化，但其受进化约束的程度高于mRNA（messenger RNA，信使RNA）水平。对蛋白质组开展模块级比较分析后发现，表达水平更高的蛋白质往往保守性更强。为解析进化保守与分化的模式，本研究开发了一套全新的整合分析流程，该流程结合公开可用的转录组数据集以定义共表达（co-expression）模块。本分析流程可用于关联蛋白质表达水平变化与不同物种特有的表型（phenotypic）性状。本研究以根瘤菌-豆科植物共生（rhizobia-legume symbiosis）过程为例开展案例分析，证实了自噬（autophagy）与氧化还原调控（redox management）过程在该共生关系中的关键作用。