ArticleeLife2020
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.
Article in eLife, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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90 citing papers in PubMed, 167 citations in OpenAlex.
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- Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome.Genome biology and evolution · 2026Article
- Biological foundation models illuminate annotation blind spots in evolutionarily divergent genomes.bioRxiv : the preprint server for biology · 2026Article
- Deep homology and design of proteasome chaperone proteins in Candidozyma auris.Nature communications · 2026Article
- Origin of class B J-domain proteins involved in amyloid transactions.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition.Bioinformatics advances · 2026Article
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- Genomic resources for the scuttle fly Megaselia abdita: a model organism for comparative developmental studies in flies.Development (Cambridge, England) · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation.Bioinformatics (Oxford, England) · 2025Article
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- Genomic Analysis Reveals the Role of New Genes in Venom Regulatory Network of Parasitoid Wasps.Insects · 2025Article
- Identification of a Highly VirulentPlants (Basel, Switzerland) · 2025Article
- Unbiased anchors for reliable genome-wide synteny detection.Algorithms for molecular biology : AMB · 2025Article
- Functional innovation through new genes as a general evolutionary process.Nature genetics · 2025Review
- Candidate orphan genes: Reassessing uniqueness.PloS one · 2025Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The origin of 'orphan' genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist. The relative contribution of the two processes remains unknown. Here, we harness the special circumstance of conserved synteny to estimate the contribution of complete divergence to the pool of orphan genes. By separately comparing yeast, fly and human genes to related taxa using conservative criteria, we find that complete divergence accounts, on average, for at most a third of eukaryotic orphan and taxonomically restricted genes. We observe that complete divergence occurs at a stable rate within a phylum but at different rates between phyla, and is frequently associated with gene shortening akin to pseudogenization.
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