| On the origin of de novo genes in arabidopsis thaliana populations | |
| Li, Zi-Wen1; Chen, Xi1,2; Wu, Qiong1; Hagmann, Joerg3; Han, Ting-Shen1,2; Zou, Yu-Pan1,2; Ge, Song1; Guo, Ya-Long1 | |
| 刊名 | Genome biology and evolution
 |
| 2016-07-01 | |
| 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 |
| 通讯作者 | Guo, ya-long(yalong.guo@ibcas.ac.cn) |
| 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. |
| WOS关键词 | LINEAGE-SPECIFIC GENES ; OPEN READING FRAMES ; TRANSPOSABLE ELEMENTS ; DROSOPHILA-MELANOGASTER ; PROTEIN FAMILIES ; DNA METHYLATION ; ORPHAN GENES ; SMALL RNA ; EVOLUTION ; GENOME |
| WOS研究方向 | Evolutionary Biology ; Genetics & Heredity |
| WOS类目 | Evolutionary Biology ; Genetics & Heredity |
| 语种 | 英语 |
| 出版者 | OXFORD UNIV PRESS |
| WOS记录号 | WOS:000381502000010 |
| 内容类型 | 期刊论文 |
| URI标识 | http://www.corc.org.cn/handle/1471x/2374380 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Guo, Ya-Long |
| 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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