ArticleGenome biology and evolution2016
On the Origin of De Novo Genes in Arabidopsis thaliana Populations.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 64 citations in OpenAlex.
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Emergence and Tandem Repeat-Mediated Elongation of a Translated De Novo Open Reading Frame in Human Oncogenic RNA Gene VPS9D1-AS1 (MYU).Genome biology and evolution · 2026Article
- Comparative analysis of m6A mRNA modification inFrontiers in genetics · 2026Article
- Article
- Improved sampling of genotypes and species reveals new insights on de novo gene history and regulatory origins.Genetics · 2025Article
- Genome assembly of Stewartia sinensis reveals origin and evolution of orphan genes in Theaceae.Communications biology · 2025Article
- Functional innovation through new genes as a general evolutionary process.Nature genetics · 2025Review
- A de novo Gene Promotes Seed Germination Under Drought Stress in Arabidopsis.Molecular biology and evolution · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Article
- The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.Genome biology · 2024Article
- A putative scenario of how de novo protein-coding genes originate in the Saccharomyces cerevisiae lineage.BMC genomics · 2024Article
- High Polymorphism Levels of De Novo ORFs in a Yoruba Human Population.Genome biology and evolution · 2024Article
- A de novo evolved gene contributes to rice grain shape difference between indica and japonica.Nature communications · 2023Article
- Towards understanding paleoclimate impacts on primate de novo genes.G3 (Bethesda, Md.) · 2023Article
- Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inGenome research · 2023Article
- Molecular mechanisms of adaptive evolution in wild animals and plants.Science China. Life sciences · 2023Review
- The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution.Plant communications · 2023Article
- Article
- Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.