Wide-Spread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

Gene duplications (GDs) provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses on 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms, to detect large-scale gene duplication events by survey of tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses here detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaption to environmental changes.

基因复制可以为物种产生新的功能提供演化上的潜力，而多倍化事件或全基因组复制事件直接将染色体进行加倍，可能会保留数百到数千个复制单位。在真核生物许多物种丰富的谱系中均检测到了全基因组复制事件的发生，因此我们认为其是一种驱动物种分化的主要动力。本文，作者对大部分被子植物谱系的59个已测序基因组或转录组植物及另外46个新测转录组植物进行了比较基因组及系统基因组的分析，通过数以万计的基因家族进化树的构建大范围地检测基因复制事件。这些分析确定了现前大多数的全基因组复制事件的研究，同时提供了强有力的证据表明在一些谱系中存在之前未能检测到的全基因组复制事件。数据显示在进化过程中，全基因组复制事件得到的复制基因会以大约21.6个百万年的半衰期呈指数式的衰减，同时基因的丢失速率还与新谱系的形成、分化程度的高度及全球气候变化的时期相关。这些新的数据及分析检测到了被子植物在进化过程中许多新的全基因组复制事件，揭示了在基本细胞代谢方面起作用的基因的优先保留，为全基因组复制事件在促进被子植物辐射及增强其对环境变化的适应过程中所扮演的重要作用提供线索。

通讯：戚继 (http://life.fudan.edu.cn/Data/View/1393)

个人简介：1995-1999年，吉林大学，物理系，学士；1999-2004年，中国科学院理论物理研究所，博士；2005-2010年，美国宾州州立大学，比较基因组学和生物信息学中心，博士后。

doi: http://dx.doi.org/10.1016/j.molp.2018.01.002