Sequential Paleotetraploidization shaped the carrot genome

doi:10.1186/s12870-020-2235-7

	Sequential Paleotetraploidization shaped the carrot genome
	Wang, Jinpeng 1,2,5; Yu, Jigao ; Li, Yuxian ; Wei, Chendan ; Guo, He ; Liu, Ying ; Zhang, Jin ; Li, Xiuqing 3; Wang, Xiyin 4
	2020
发表期刊	BMC PLANT BIOLOGY
ISSN	1471-2229
卷号	20 期号:1
摘要	Background Carrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined. Results Using a previously published comparative genomics pipeline, we reanalysed the carrot genome and characterized genomic fractionation, as well as gene loss and retention, after each of the two tetraploidization events and inferred a dominant and sensitive subgenome for each event. In particular, we found strong evidence of two sequential tetraploidization events, with one (Dc-alpha) approximately 46-52 million years ago (Mya) and the other (Dc-beta) approximately 77-87 Mya, both likely allotetraploidization in nature. The Dc-beta event was likely common to all Apiales plants, occurring around the divergence of Apiales-Bruniales and after the divergence of Apiales-Asterales, likely playing an important role in the derivation and divergence of Apiales species. Furthermore, we found that rounds of polyploidy events contributed to the expansion of gene families responsible for plastidial methylerythritol phosphate (MEP), the precursor of carotenoid accumulation, and shaped underlying regulatory pathways. The alignment of orthologous and paralogous genes related to different events of polyploidization and speciation constitutes a comparative genomics platform for studying Apiales, Asterales, and many other related species. Conclusions Hierarchical inference of homology revealed two tetraploidization events that shaped the carrot genome, which likely contributed to the successful establishment of Apiales plants and the expansion of MEP, upstream of the carotenoid accumulation pathway.
关键词	Carrot Coffee Lettuce Carotenoids Gene collinearity Genomic fractionation Polyploidization
学科领域	Plant Sciences
DOI	10.1186/s12870-020-2235-7
收录类别	SCI
语种	英语
WOS关键词	EVOLUTION ; GENE ; DUPLICATION ; ANCIENT ; POLYPLOIDIZATION ; ESTABLISHES ; SUBGENOMES ; ALIGNMENT ; ANCESTOR ; PROVIDES
WOS研究方向	Plant Sciences
WOS记录号	WOS:000513146200003
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	Ministry of Science and Technology of the People's Republic of ChinaMinistry of Science and Technology, China [2016YFD0101001] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31371282, 31510333, 31661143009] ; National Natural Science Foundation of Hebei Province [C2015209069] ; Tangshan Key Laboratory
作者邮箱	wangxiyin@vip.sina.com
引用统计	被引频次：6[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/21915
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, Ctr Genom & Computat Biol, Sch Life Sci, Tangshan 063200, Hebei, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Agr & Agri Food Canada, Fredericton Res & Dev Ctr, Fredericton, NB E3B 4Z7, Canada 5.Chengdu Univ Tradit Chinese Med, Sch Genom & Biobig Data, Chengdu 610075, Peoples R China 6.Handan Univ, Coll Math & Sci, Handan 056005, Hebei, Peoples R China
推荐引用方式 GB/T 7714	Wang, Jinpeng,Yu, Jigao,Li, Yuxian,et al. Sequential Paleotetraploidization shaped the carrot genome[J]. BMC PLANT BIOLOGY,2020,20(1).
APA	Wang, Jinpeng.,Yu, Jigao.,Li, Yuxian.,Wei, Chendan.,Guo, He.,...&Wang, Xiyin.(2020).Sequential Paleotetraploidization shaped the carrot genome.BMC PLANT BIOLOGY,20(1).
MLA	Wang, Jinpeng,et al."Sequential Paleotetraploidization shaped the carrot genome".BMC PLANT BIOLOGY 20.1(2020).

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