McGrath Casey L, Gout Jean-Francois, Doak Thomas G, Yanagi Akira, Lynch Michael
Department of Biology, Indiana University.
Department of Biology, Indiana University National Center for Genome Analysis Support at Indiana University, Bloomington, Indiana 47405.
Genetics. 2014 Aug;197(4):1417-28. doi: 10.1534/genetics.114.163287. Epub 2014 May 19.
Paramecium has long been a model eukaryote. The sequence of the Paramecium tetraurelia genome reveals a history of three successive whole-genome duplications (WGDs), and the sequences of P. biaurelia and P. sexaurelia suggest that these WGDs are shared by all members of the aurelia species complex. Here, we present the genome sequence of P. caudatum, a species closely related to the P. aurelia species group. P. caudatum shares only the most ancient of the three WGDs with the aurelia complex. We found that P. caudatum maintains twice as many paralogs from this early event as the P. aurelia species, suggesting that post-WGD gene retention is influenced by subsequent WGDs and supporting the importance of selection for dosage in gene retention. The availability of P. caudatum as an outgroup allows an expanded analysis of the aurelia intermediate and recent WGD events. Both the Guanine+Cytosine (GC) content and the expression level of preduplication genes are significant predictors of duplicate retention. We find widespread asymmetrical evolution among aurelia paralogs, which is likely caused by gradual pseudogenization rather than by neofunctionalization. Finally, cases of divergent resolution of intermediate WGD duplicates between aurelia species implicate this process acts as an ongoing reinforcement mechanism of reproductive isolation long after a WGD event.
草履虫长期以来一直是真核生物的模型。四膜虫的基因组序列揭示了三次连续全基因组复制（WGD）的历史，双小核草履虫和六小核草履虫的序列表明，这些WGD为所有双小核草履虫物种复合体的成员所共有。在此，我们展示了尾草履虫的基因组序列，它是一种与双小核草履虫物种组密切相关的物种。尾草履虫与双小核草履虫复合体仅共享三次WGD中最古老的那次。我们发现，尾草履虫从这一早期事件中保留的旁系同源基因数量是双小核草履虫物种的两倍，这表明WGD后的基因保留受到后续WGD的影响，并支持了基因保留中剂量选择的重要性。尾草履虫作为外类群的可用性使得对双小核草履虫中间和近期WGD事件的分析得以扩展。鸟嘌呤 + 胞嘧啶（GC）含量和复制前基因的表达水平都是重复基因保留的重要预测指标。我们发现双小核草履虫旁系同源基因之间存在广泛的不对称进化，这可能是由渐进的假基因化而非新功能化导致的。最后，双小核草履虫物种之间中间WGD重复基因的分歧解析案例表明，这一过程在WGD事件发生很久之后，仍作为生殖隔离的持续强化机制发挥作用。
