On the Origin of De Novo Genes in Arabidopsis thaliana Populations

doi:10.1093/gbe/evw164

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	On the Origin of De Novo Genes in Arabidopsis thaliana Populations
	Li, Zi-Wen ; Chen, Xi ; Wu, Qiong ; Hagmann, Joerg 2; Han, Ting-Shen ; Zou, Yu-Pan ; Ge, Song ; Guo, Ya-Long
刊名	GENOME BIOLOGY AND EVOLUTION
	2016
卷号	8 期号:7 页码:2190-2202
关键词	de novo genes DNA methylation origin process protein-coding genes
ISSN号	1759-6653
DOI	10.1093/gbe/evw164
文献子类	Article
英文摘要	De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications ( DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process.
学科主题	Evolutionary Biology ; Genetics & Heredity
出版地	OXFORD
WOS关键词	LINEAGE-SPECIFIC GENES ; OPEN READING FRAMES ; TRANSPOSABLE ELEMENTS ; DROSOPHILA-MELANOGASTER ; DNA METHYLATION ; GENOME ; EVOLUTION ; RNA ; IDENTIFICATION ; GENERATION
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000381502000010
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [91231104, 31222006, 31470331] ; 100 Talents Program of the Chinese Academy
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/24998]
专题	系统与进化植物学国家重点实验室
作者单位	1.Max Planck Inst Dev Biol, Dept Mol Biol, Tubingen, Germany 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Li, Zi-Wen,Chen, Xi,Wu, Qiong,et al. On the Origin of De Novo Genes in Arabidopsis thaliana Populations[J]. GENOME BIOLOGY AND EVOLUTION,2016,8(7):2190-2202.
APA	Li, Zi-Wen.,Chen, Xi.,Wu, Qiong.,Hagmann, Joerg.,Han, Ting-Shen.,...&Guo, Ya-Long.(2016).On the Origin of De Novo Genes in Arabidopsis thaliana Populations.GENOME BIOLOGY AND EVOLUTION,8(7),2190-2202.
MLA	Li, Zi-Wen,et al."On the Origin of De Novo Genes in Arabidopsis thaliana Populations".GENOME BIOLOGY AND EVOLUTION 8.7(2016):2190-2202.