ArticleGenome biology and evolution2013
Mechanisms and dynamics of orphan gene emergence in insect genomes.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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93 citing papers in PubMed.
- DetectNAR genomics and bioinformatics · 2026Article
- Reduced Detection of Human Orphan Gene Transcripts in Disease Tissue Relative to Expression- and Detection- Matched Controls.Biology · 2026Article
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- A compendium of horizontal gene transfers in Metazoa.Scientific data · 2026Article
- Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster.Molecular biology and evolution · 2026Article
- Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition.Bioinformatics advances · 2026Article
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- The eukaryotic horizontal gene transfer dataset a compendium.bioRxiv : the preprint server for biology · 2025Article
- DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation.Bioinformatics (Oxford, England) · 2025Article
- Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution.Molecular biology and evolution · 2025Article
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
- Identification of a Highly VirulentPlants (Basel, Switzerland) · 2025Article
- Article
- 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
- An Orphan Gene Enhances Male Reproductive Success in Plutella xylostella.Molecular biology and evolution · 2024Article
- Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences.Molecular genetics and genomics : MGG · 2024Article
- Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution.Development genes and evolution · 2023Review
- Combined Transcriptome and Proteome Analysis of the Protein Composition of the Brochosomes of the LeafhopperInsects · 2023Article
- Facing lethal temperatures: Heat-shock response in desert and temperate ants.Ecology and evolution · 2023Article
33 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all genes in a genome. Several case studies demonstrated that orphans can contribute to lineage-specific adaptation. Here, we study orphan genes by comparing 30 arthropod genomes, focusing in particular on seven recently sequenced ant genomes. This setup allows analyzing a major metazoan taxon and a comparison between social Hymenoptera (ants and bees) and nonsocial Diptera (flies and mosquitoes). First, we find that recently split lineages undergo accelerated genomic reorganization, including the rapid gain of many orphan genes. Second, between the two insect orders Hymenoptera and Diptera, orphan genes are more abundant and emerge more rapidly in Hymenoptera, in particular, in leaf-cutter ants. With respect to intragenomic localization, we find that ant orphan genes show little clustering, which suggests that orphan genes in ants are scattered uniformly over the genome and between nonorphan genes. Finally, our results indicate that the genetic mechanisms creating orphan genes-such as gene duplication, frame-shift fixation, creation of overlapping genes, horizontal gene transfer, and exaptation of transposable elements-act at different rates in insects, primates, and plants. In Formicidae, the majority of orphan genes has their origin in intergenic regions, pointing to a high rate of de novo gene formation or generalized gene loss, and support a recently proposed dynamic model of frequent gene birth and death.
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