Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies

doi:10.1016/j.xplc.2022.100427

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	Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies
	Yin,Xin; Yang,Danni; Zhao,Youjie; Yang,Xingyu; Zhou,Zhili; Sun,Xudong; Kong,Xiangxiang; Li,Xiong; Wang,Guangyan; Duan,Yuanwen; Yang,Yunqiang; Yang,Yongping
	2023
发表期刊	PLANT COMMUNICATIONS
卷号	4 期号:1 页码:100427
摘要	Pseudogenes are important resources for investigation of genome evolution and genomic diversity because they are nonfunctional but have regulatory effects that influence plant adaptation and diversification. However, few systematic comparative analyses of pseudogenes in closely related species have been conducted. Here, we present a turnip (Brassica rapa ssp. rapa) genome sequence and characterize pseudogenes among diploid Brassica species/subspecies. The results revealed that the number of pseudogenes was greatest in Brassica oleracea (CC genome), followed by B. rapa (AA genome) and then Brassica nigra (BB genome), implying that pseudogene differences emerged after species differentiation. In Brassica AA genomes, pseudogenes were distributed asymmetrically on chromosomes because of numerous chromosomal insertions/rearrangements, which contributed to the diversity among subspecies. Pseudogene differences among subspecies were reflected in the flavor-related glucosinolate (GSL) pathway. Specifically, turnip had the highest content of pungent substances, probably because of expansion of the methylthioalkylmalate synthase-encoding gene family in turnips; these genes were converted into pseudogenes in B. rapa ssp. pekinensis (Chiifu). RNA interference-based silencing of the gene encoding 2-oxoglutarate-dependent dioxygenase 2, which is also associated with flavor and anticancer substances in the GSL pathway, resulted in increased abundance of anticancer compounds and decreased pungency of turnip and Chiifu. These findings revealed that pseudogene differences between turnip and Chiifu influenced the evolution of flavor-associated GSL metabolism-related genes, ultimately resulting in the different flavors of turnip and Chiifu.
关键词	turnip genome comparative genomics pseudogene evolution GSL biosynthesis flavor Brassicaceae lineage -specific polyploidization events (whole WHOLE-GENOME TRIPLICATION PHYLOGENETIC ANALYSIS GLUCOSINOLATE CONTENT ARABIDOPSIS IDENTIFICATION OLERACEA EXPRESSION SEQUENCE ORIGIN DIVERSIFICATION
学科领域	Biochemistry & Molecular Biology ; Plant Sciences
DOI	10.1016/j.xplc.2022.100427
收录类别	SCI
WOS记录号	WOS:000925059200001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75385
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Yin,Xin,Yang,Danni,Zhao,Youjie,et al. Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies[J]. PLANT COMMUNICATIONS,2023,4(1):100427.
APA	Yin,Xin.,Yang,Danni.,Zhao,Youjie.,Yang,Xingyu.,Zhou,Zhili.,...&Yang,Yongping.(2023).Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies.PLANT COMMUNICATIONS,4(1),100427.
MLA	Yin,Xin,et al."Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies".PLANT COMMUNICATIONS 4.1(2023):100427.

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