ArticleMolecular biology and evolution2018
A Molecular Portrait of De Novo Genes in Yeasts.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- DetectNAR genomics and bioinformatics · 2026Article
- Emergence Biases in Molecular Evolution.Genome biology and evolution · 2026Review
- 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
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- Comparative analysis of m6A mRNA modification inFrontiers in genetics · 2026Article
- Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition.Bioinformatics advances · 2026Article
- De Novo Genes: Current Status and Future Goals.Genome biology and evolution · 2025Article
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- Chasing the Ghost Proteome in the Dark Matter.Molecular & cellular proteomics : MCP · 2025Review
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
- Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.Cell genomics · 2025Article
- Improved sampling of genotypes and species reveals new insights on de novo gene history and regulatory origins.Genetics · 2025Article
- The hidden bacterial microproteome.Molecular cell · 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
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa.Molecular ecology · 2024Article
- Article
23 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo gene candidates in 15 yeast species from 2 genera whose phylogeny spans at least 100 million years of evolution. We validated 85 candidates by proteomic data, providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from noncoding to coding for 30 Saccharomyces de novo genes. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We also found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. Finally, we found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination contributes to de novo gene emergence in yeasts.
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