Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades

doi:10.3389/fpls.2022.883140

	Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades
	Teng, Jia 2; Wang, Jianyu 2; Zhang, Lan 2; Wei, Chendan 2; Shen, Shaoqi 2; Xiao, Qimeng 2; Yue, Yuanshuai 2; Hao, Yanan 2; Ge, Weina 2; Wang, Jinpeng 1,2
	2022
发表期刊	FRONTIERS IN PLANT SCIENCE
ISSN	1664-462X
卷号	13
摘要	Eudicots account for ~75% of living angiosperms, containing important food and energy crops. Recently, high-quality genome sequences of several eudicots including Aquilegia coerulea and Nelumbo nucifera have become available, providing an opportunity to investigate the early evolutionary characteristics of eudicots. We performed genomic hierarchical and event-related alignments to infer homology within and between representative species of eudicots. The results provide strong evidence for multiple independent polyploidization events during the early diversification of eudicots, three of which are likely to be allopolyploids: The core eudicot-common hexaploidy (ECH), Nelumbo-specific tetraploidy (NST), and Ranunculales-common tetraploidy (RCT). Using different genomes as references, we constructed genomic alignment to list the orthologous and paralogous genes produced by polyploidization and speciation. This could provide a fundamental framework for studying other eudicot genomes and gene(s) evolution. Further, we revealed significantly divergent evolutionary rates among these species. By performing evolutionary rate correction, we dated RCT to be ~118-134 million years ago (Mya), after Ranunculales diverged with core eudicots at ~123-139 Mya. Moreover, we characterized genomic fractionation resulting from gene loss and retention after polyploidizations. Notably, we revealed a high degree of divergence between subgenomes. In particular, synonymous nucleotide substitutions at synonymous sites (Ks) and phylogenomic analyses implied that A. coerulea might provide the subgenome(s) for the gamma-hexaploid hybridization.
关键词	Aquilegia coerulea Nelumbo nucifera Vitis vinifera hierarchical alignment gene colinearity polyploidization
学科领域	Plant Sciences
DOI	10.3389/fpls.2022.883140
收录类别	SCI
语种	英语
WOS关键词	EVOLUTIONARY SIGNIFICANCE ; PHYLOGENETIC ANALYSIS ; POLYPLOIDY ; ANCIENT ; SEQUENCE ; GENES ; DIVERSIFICATION ; DUPLICATION ; DIVERGENCE ; MECHANISMS
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000810934700001
出版者	FRONTIERS MEDIA SA
文献子类	Article
出版地	LAUSANNE
作者邮箱	gwn-06@163.com ; wangjinpeng@ibcas.ac.cn
作品OA属性	Green Published, gold
引用统计
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28884
专题	系统与进化植物学国家重点实验室
作者单位	1.North China Univ Sci & Technol, Sch Life Sci, Dept Bioinformat, Tangshan, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 3.North China Univ Sci & Technol, Ctr Genom & Computat Biol, Dept Bioinformat, Tangshan, Peoples R China
推荐引用方式 GB/T 7714	Teng, Jia,Wang, Jianyu,Zhang, Lan,et al. Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades[J]. FRONTIERS IN PLANT SCIENCE,2022,13.
APA	Teng, Jia.,Wang, Jianyu.,Zhang, Lan.,Wei, Chendan.,Shen, Shaoqi.,...&Wang, Jinpeng.(2022).Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades.FRONTIERS IN PLANT SCIENCE,13.
MLA	Teng, Jia,et al."Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades".FRONTIERS IN PLANT SCIENCE 13(2022).

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