Instituto de Biologia Molecular y Celular de Plantas-IBMCP (CSIC-UPV), Integrative Systems Biology Group, Valencia, Spain.
Mol Biol Evol. 2012 Nov;29(11):3541-51. doi: 10.1093/molbev/mss162. Epub 2012 Jun 24.
Gene duplicates are a major source of evolutionary novelties in the form of new or specialized functions and play a key role in speciation. Gene duplicates are generated through whole genome duplications (WGD) or small-scale genome duplications (SSD). Although WGD preserves the stoichiometric relationships between duplicates, those arising from SSD are usually unbalanced and are expected to follow different evolutionary dynamics than those formed by WGD. To dissect the role of the mechanism of duplication in these differential dynamics and determine whether this role was shared across species, we performed a genome wide evolutionary analysis of gene duplications arising from the most recent WGD events and contemporary episodes of SSD in four model species representing distinct plant evolutionary lineages. We found an excess of relaxed purifying selection after duplication in SSD paralogs compared with WGD, most of which may have been the result of functional divergence events between gene copies as estimated by measures of genetic distances. These differences were significant in three angiosperm genomes but not in the moss species Physcomitrella patens. Although the comparison of models of evolution does not attribute a relevant role to the mechanism of duplication in the evolution duplicates, distribution of retained genes among Gene Ontology functional categories support the conclusion that evolution of gene duplicates depends on its origin of duplication (WGD and SSD) but, most importantly, on the species. Similar lineage-specific biases were also observed in protein network connectivity, translational efficiency, and selective constraints acting on synonymous codon usage. Although the mechanism of duplication may determine gene retention, our results attribute a dominant role to the species in determining the ultimate pattern of duplicate gene retention and reveal an unanticipated complexity in the evolutionary dynamics and functional specialization of duplicated genes in plants.
基因复制是形成新的或特化功能的进化新事物的主要来源，在物种形成中起着关键作用。基因复制是通过全基因组复制（WGD）或小规模基因组复制（SSD）产生的。虽然 WGD 保留了复制体之间的化学计量关系，但那些来自 SSD 的复制体通常是不平衡的，预计其进化动态与 WGD 形成的复制体不同。为了剖析复制机制在这些差异进化动态中的作用，并确定这种作用是否在物种间共享，我们对四个代表不同植物进化谱系的模型物种中最近发生的 WGD 事件和当代 SSD 事件产生的基因复制进行了全基因组进化分析。我们发现，与 WGD 相比，SSD 同源基因在复制后经历了过度放松的纯化选择，其中大部分可能是由于基因拷贝之间的功能分化事件，这是通过遗传距离衡量来估计的。这些差异在三个被子植物基因组中很显著，但在藓类植物 Physcomitrella patens 中并不显著。尽管对进化模型的比较并没有将复制机制归因于进化复制的相关作用，但保留基因在基因本体论功能类别中的分布支持了这样的结论，即基因复制的进化取决于其复制的起源（WGD 和 SSD），但最重要的是取决于物种。在蛋白质网络连接性、翻译效率和对同义密码子使用的选择约束方面，也观察到类似的谱系特异性偏倚。尽管复制机制可能决定基因保留，但我们的结果将物种归因于决定基因重复保留的最终模式，并揭示了植物中重复基因的进化动态和功能特化的预期之外的复杂性。
