Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms  

作　　者：Ren Ren Haifeng Wang Chunce Guo Ning Zhang Liping Zeng Yamao Chen Hong Ma Ji Qi 

机构地区：[1]State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China [2]State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China [3]Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA [4]Institutes of Biomedical Sciences, Fudan University, Shanghai, China [5]These authors contributed equally to this article.

出　　处：《Molecular Plant》2018年第3期414-428,共15页分子植物（英文版）

摘　　要：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 per- formed 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 dupli- cation 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 approx- imately 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.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 per- formed 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 dupli- cation 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 approx- imately 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.

关 键 词：whole genome duplication duplicate gene POLYPLOIDIZATION ANGIOSPERM PHYLOGENOMICS 

分 类 号：Q949.7[生物学—植物学] S511.03[农业科学—作物学]