Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms
Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms
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广泛的全基因组重复导致被子植物的基因组复杂性和物种多样性
DOI：
10.1016/j.molp.2018.01.002
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发表时间：
2018-03-05
期刊：
影响因子：
27.5
通讯作者：
Qi, Ji
中科院分区：
文献类型：
--
作者：
Ren, Ren;Wang, Haifeng;Qi, Ji
基因复制为产生新功能提供了进化潜力，而多倍体化或全基因组复制（WGD）最初使染色体加倍，并产生数百至数千个保留的重复。在许多真核生物物种丰富的谱系中普遍发现的证据强烈支持WGDs，因此被认为是物种多样化的主要驱动力。我们对覆盖被子植物主要谱系的59个公开基因组/转录组和46个新测序的转录组进行了比较基因组学和系统基因组学分析，通过调查数万个基因家谱来检测大规模的基因重复事件。这些分析证实了大多数以前报道的WGDs，并为许多世系中新的WGDs提供了强有力的证据。检测到的WGDs支持了进化过程中指数基因损失的模型，估计半衰期约为2160万年，并且与高度多样化谱系的出现和全球气候变化时期相关。新的数据集和分析发现了在被子植物进化过程中广泛分布的许多新的WGD，揭示了基因功能在细胞必需代谢中的优先保留，并为WGD在促进被子植物辐射和增强其对环境变化的适应方面的作用提供了线索。
Gene duplications 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, and thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying 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 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 adaptation to environmental changes.