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Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms.
Mol Plant. 2018 03 05; 11(3):414-428.MP

Abstract

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.

Authors+Show Affiliations

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.State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.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.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; Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA.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.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.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; Institutes of Biomedical Sciences, Fudan University, Shanghai, China. Electronic address: hongma@fudan.edu.cn.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. Electronic address: qij@fudan.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29317285

Citation

Ren, Ren, et al. "Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms." Molecular Plant, vol. 11, no. 3, 2018, pp. 414-428.
Ren R, Wang H, Guo C, et al. Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms. Mol Plant. 2018;11(3):414-428.
Ren, R., Wang, H., Guo, C., Zhang, N., Zeng, L., Chen, Y., Ma, H., & Qi, J. (2018). Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms. Molecular Plant, 11(3), 414-428. https://doi.org/10.1016/j.molp.2018.01.002
Ren R, et al. Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms. Mol Plant. 2018 03 5;11(3):414-428. PubMed PMID: 29317285.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms. AU - Ren,Ren, AU - Wang,Haifeng, AU - Guo,Chunce, AU - Zhang,Ning, AU - Zeng,Liping, AU - Chen,Yamao, AU - Ma,Hong, AU - Qi,Ji, Y1 - 2018/01/06/ PY - 2017/11/08/received PY - 2017/12/13/revised PY - 2018/01/02/accepted PY - 2018/1/11/pubmed PY - 2018/12/12/medline PY - 2018/1/11/entrez KW - angiosperm KW - duplicate gene KW - phylogenomics KW - polyploidization KW - whole genome duplication SP - 414 EP - 428 JF - Molecular plant JO - Mol Plant VL - 11 IS - 3 N2 - 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. SN - 1752-9867 UR - https://www.unboundmedicine.com/medline/citation/29317285/Widespread_Whole_Genome_Duplications_Contribute_to_Genome_Complexity_and_Species_Diversity_in_Angiosperms_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1674-2052(18)30022-4 DB - PRIME DP - Unbound Medicine ER -