ArticleMolecular biology and evolution2023
Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 27 citations in OpenAlex.
- Review
- DetectNAR genomics and bioinformatics · 2026Article
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster.Molecular biology and evolution · 2026Article
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- Multiple human enhancer RNAs contain long translated open reading frames.Genes & development · 2025Article
- Multiple human enhancer RNAs contain long translated open reading frames.Genes & development · 2025Article
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation.Bioinformatics (Oxford, England) · 2025Article
- Improved sampling of genotypes and species reveals new insights on de novo gene history and regulatory origins.Genetics · 2025Article
- Gene age and genome organization inFrontiers in microbiology · 2025Article
- Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.Genome research · 2024Article
- How antisense transcripts can evolve to encode novel proteins.Nature communications · 2024Article
- Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution.Genome biology and evolution · 2024Article
- DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs.Genome biology and evolution · 2024Article
- Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New protein coding genes can emerge from genomic regions that previously did not contain any genes, via a process called de novo gene emergence. To synthesize a protein, DNA must be transcribed as well as translated. Both processes need certain DNA sequence features. Stable transcription requires promoters and a polyadenylation signal, while translation requires at least an open reading frame. We develop mathematical models based on mutation probabilities, and the assumption of neutral evolution, to find out how quickly genes emerge and are lost. We also investigate the effect of the order by which DNA features evolve, and if sequence composition is biased by mutation rate. We rationalize how genes are lost much more rapidly than they emerge, and how they preferentially arise in regions that are already transcribed. Our study not only answers some fundamental questions on the topic of de novo emergence but also provides a modeling framework for future studies.
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