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On the Origin of De Novo Genes in Arabidopsis thaliana Populations | |
Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Joerg2; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long | |
2016 | |
发表期刊 | GENOME BIOLOGY AND EVOLUTION |
ISSN | 1759-6653 |
卷号 | 8期号:7页码:2190-2202 |
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. |
关键词 | de novo genes DNA methylation origin process protein-coding genes |
学科领域 | Evolutionary Biology ; Genetics & Heredity |
DOI | 10.1093/gbe/evw164 |
收录类别 | SCI |
语种 | 英语 |
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) |
WOS记录号 | WOS:000381502000010 |
出版者 | OXFORD UNIV PRESS |
文献子类 | Article |
出版地 | OXFORD |
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 |
作者邮箱 | yalong.guo@ibcas.ac.cn |
作品OA属性 | Green Published, gold, Green Submitted |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | 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.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Max Planck Inst Dev Biol, Dept Mol Biol, Tubingen, Germany |
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. |
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