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,fe...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.展开更多
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences,Pan-Third Pole Environment Study for a Green Silk Road(Pan-TPE)(XDA2004010306)the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)+6 种基金the National Natural Science Foundation of China(32070362,41771123,and 32100315)the“Cross-Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciencesthe Natural Science Foundation of Yunnan Province(202101AT070190)Digitalization,Development,and Application of Biotic Resource(202002AA100007)the Poverty Alleviation through Science and Technology Projects of the Chinese Academy of Sciences(KFJ-FP-201905)the Technology Transfer into Yunnan Project(202003AD150005)the Postdoctoral Research Funding Projects of Yunnan Province(to X.Yin).
文摘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.
