On the Origin of De Novo Genes in Arabidopsis thaliana Populations.
On the Origin of De Novo Genes in Arabidopsis thaliana Populations.
复制标题
拟南芥种群 De Novo 基因的起源
DOI：
10.1093/gbe/evw164
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发表时间：
2016-08-03
影响因子：
3.3
通讯作者：
Guo YL
中科院分区：
文献类型：
--
作者：
Li ZW;Chen X;Wu Q;Hagmann J;Han TS;Zou YP;Ge S;Guo YL
摘要从头基因是蛋白质编码基因的重要来源之一，起源于祖先的非基因序列。这种起源过程对生物体的适应至关重要。然而，从头基因如何产生并固定在种群或物种中仍然是未知的。在这里，我们从模式植物拟南芥中鉴定了782个从头基因，并根据其来源的翻译证据、转录证据和既不转录也不翻译证据的可用性将它们分为三种类型。重要的是，通过整合多种类型的组学数据，包括来自基因组、表观基因组、转录组和翻译组的数据，我们发现表观遗传修饰（DNA甲基化和组蛋白修饰）在从头基因的起源过程中起着重要作用。有趣的是，使用来自84个加入物的相同群体的转录组和甲基化组，我们发现在群体内大约一半的总加入物中转录的从头基因是高度甲基化的，转录水平低于群体内以其他频率转录的基因。我们假设，在从头基因等位基因的起源过程中，那些通过DNA甲基化被中和到低表达状态的等位基因在人群中传播和固定的概率相对较高。我们的研究结果强调了在群体水平上从头基因起源的过程，以及DNA甲基化在这一过程中的重要性。
Abstract 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.