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Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes
Xu, Yong-Chao; Niu, Xiao-Min; Li, Xin-Xin; He, Wenrong2; Chen, Jia-Fu; Zou, Yu-Pan; Wu, Qiong; Zhang, Yong E.; Busch, Wolfgang2; Guo, Ya-Long
2019
发表期刊PLANT CELL
ISSN1040-4651
卷号31期号:5页码:1012-1025
摘要According to the less-is-more hypothesis, gene loss is an engine for evolutionary change. Loss-of-function (LoF) mutations resulting in the natural knockout of protein-coding genes not only provide information about gene function but also play important roles in adaptation and phenotypic diversification. Although the less-is-more hypothesis was proposed two decades ago, it remains to be explored on a large scale. In this study, we identified 60,819 LoF variants in 1071 Arabidopsis (Arabidopsis thaliana) genomes and found that 34% of Arabidopsis protein-coding genes annotated in the Columbia-0 genome do not have any LoF variants. We found that nucleotide diversity, transposable element density, and gene family size are strongly correlated with the presence of LoF variants. Intriguingly, 0.9% of LoF variants with minor allele frequency larger than 0.5% are associated with climate change. In addition, in the Yangtze River basin population, 1% of genes with LoF mutations were under positive selection, providing important insights into the contribution of LoF mutations to adaptation. In particular, our results demonstrate that LoF mutations shape diverse phenotypic traits. Overall, our results highlight the importance of the LoF variants for the adaptation and phenotypic diversification of plants.
学科领域Biochemistry & Molecular Biology ; Plant Sciences ; Cell Biology
DOI10.1105/tpc.18.00791
收录类别SCI
语种英语
WOS关键词DE-NOVO GENES ; DOSAGE-SENSITIVITY ; BALANCE HYPOTHESIS ; GENOMES ; EVOLUTION ; VARIANTS ; TRANSITION ; DIVERSITY ; DISCOVERY ; HISTORY
WOS研究方向Biochemistry & Molecular Biology ; Plant Sciences ; Cell Biology
WOS记录号WOS:000467755300008
出版者OXFORD UNIV PRESS INC
文献子类Article
出版地CARY
EISSN1532-298X
资助机构Chinese Academy of SciencesChinese Academy of Sciences [XDB27010305] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [91731306] ; Salk Institute for Biological Research ; Innovative Academy of Seed Design, Chinese Academy of Sciences
作者邮箱yalong.guo@ibcas.ac.cn
作品OA属性Bronze, Green Published
引用统计
被引频次:30[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/2S10CLM1/19832
专题系统与进化植物学国家重点实验室
作者单位1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Salk Inst Biol Studies, Plant Mol & Cellular Biol Lab, La Jolla, CA 92037 USA
4.Zhang, Yong E.] Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects, Beijing, Peoples R China
5.Zhang, Yong E.] Chinese Acad Sci, Inst Zool, Rodents & Key Lab Zool Systemat & Evolut, Beijing, Peoples R China
推荐引用方式
GB/T 7714
Xu, Yong-Chao,Niu, Xiao-Min,Li, Xin-Xin,et al. Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes[J]. PLANT CELL,2019,31(5):1012-1025.
APA Xu, Yong-Chao.,Niu, Xiao-Min.,Li, Xin-Xin.,He, Wenrong.,Chen, Jia-Fu.,...&Guo, Ya-Long.(2019).Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes.PLANT CELL,31(5),1012-1025.
MLA Xu, Yong-Chao,et al."Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes".PLANT CELL 31.5(2019):1012-1025.
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