ArticleJournal of molecular evolution2020
A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila.
Article in Journal of molecular evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 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
- Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster.Molecular biology and evolution · 2026Article
- 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
- Phylostratigraphic Analysis Reveals the Evolutionary Origins and Potential Role of New Genes in the Adaptive Evolution ofInternational journal of molecular sciences · 2026Article
- Article
- Evaluating transformer-based models for structural characterization of orphan proteins.Bioinformatics advances · 2026Article
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- De Novo Genes: Current Status and Future Goals.Genome biology and evolution · 2025Article
- Recently Evolved, Stage-Specific Genes Are Enriched at Life-Stage Transitions in Flies.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Emergence of antiphage functions from random sequence libraries reveals mechanisms of gene birth.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- 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
- New perspectives on Drosophila melanogaster de novo gene origination revealed by investigation of ancient African genetic variation.Genetics · 2025Article
- An orphan gene is essential for efficient sperm entry into eggs in Drosophila melanogaster.Genetics · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- An orphan gene is essential for efficient sperm entry into eggs inbioRxiv : the preprint server for biology · 2024Article
- Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity.Genome biology and evolution · 2024Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Drosophila genus. Across the annotated proteomes of twelve species, we find 6297 orphan genes within 4953 taxon-specific clusters of orthologs. By inferring the ancestral DNA as non-coding for between 550 and 2467 (8.7-39.2%) of these genes, we describe for the first time how de novo emergence contributes to the abundance of clade-specific Drosophila genes. In support of them having functional roles, we show that de novo genes have robust expression and translational support. However, the distinct nucleotide sequences of de novo genes, which have characteristics intermediate between intergenic regions and conserved genes, reflect their recent birth from non-coding DNA. We find that de novo genes encode more disordered proteins than both older genes and intergenic regions. Together, our results suggest that gene emergence from non-coding DNA provides an abundant source of material for the evolution of new proteins. Following gene birth, gradual evolution over large evolutionary timescales moulds sequence properties towards those of conserved genes, resulting in a continuum of properties whose starting points depend on the nucleotide sequences of an initial pool of novel genes.
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