Comparative Genomics as a Time Machine: How Relative Gene Dosage and Metabolic Requirements Shaped the Time-dependent Resolution of Yeast Polyploidy
Comparative Genomics as a Time Machine: How Relative Gene Dosage and Metabolic Requirements Shaped the Time-dependent Resolution of Yeast Polyploidy
复制标题
DOI：
10.1093/molbev/msu250
复制
发表时间：
2014-12-01
影响因子：
10.7
通讯作者：
Conant, Gavin C.
中科院分区：
文献类型：
--
作者：
Conant, Gavin C.
使用基因组复制后进化的系统发育模型（即，多倍体）和12个酵母基因组与共享的基因组复制，我表明，重复基因的损失后，重复发生在三个阶段。首先，在事件发生后立即发生的损失偏向于DNA修复和细胞器功能的基因。然后，主要的重复损失组似乎是由维持蛋白质水平平衡的要求形成的：基因产物参与的蛋白质相互作用的数量与其保持重复的倾向之间存在很强的统计关联。此外，当具有相互作用的重复基因丢失时，相互作用对的两个成员在同源性的同一分支上丢失的情况比预期的更常见。最后，在解析过程的第三阶段，携带高通量的重复酶和参与转录调控的重复基因的过度保留成为主导。我推测，最初保留这些基因的要求，以维持基因剂量设置阶段，为后来的功能变化，然后保持这些重复很长一段时间。
Using a phylogenetic model of evolution after genome duplication (i.e., polyploidy) and 12 yeast genomes with a shared genome duplication, I show that the loss of duplicate genes after that duplication occurred in three phases. First, losses that occurred immediately after the event were biased toward genes functioning in DNA repair and organellar functions. Then, the main group of duplicate losses appear to have been shaped by a requirement to maintain balance in protein levels: There is a strong statistical association between the number of protein interactions a gene's product is involved in and its propensity to have remained in duplicate. Moreover, when duplicated genes with interactions were lost, it was more common than expected for both members of an interaction pair to have been lost on the same branch of the phylogeny. Finally, in the third phase of the resolution process, overretention of duplicated enzymes carrying high flux and of duplicated genes involved in transcriptional regulation became dominant. I speculate that initial retention of such genes by a requirement to maintain gene dosage set the stage for the later functional changes that then maintained these duplicates for long periods.