ArticleBMC bioinformatics2016
Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster.Molecular biology and evolution · 2026Article
- Functional innovation through new genes as a general evolutionary process.Nature genetics · 2025Review
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- Protein length distribution is remarkably uniform across the tree of life.Genome biology · 2023Article
- A survey of lineage-specific genes inPlant direct · 2023Article
- Target Selection for T-Cell Therapy in Epithelial Ovarian Cancer: Systematic Prioritization of Self-Antigens.International journal of molecular sciences · 2023Article
- ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes.PloS one · 2023Article
- Multiplex PCR Identification ofFoods (Basel, Switzerland) · 2022Article
- MultipleGenome research · 2022Article
- Research Advances and Prospects of Orphan Genes in Plants.Frontiers in plant science · 2022Review
- Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Frontiers in plant science · 2022Article
- Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution.Molecular biology and evolution · 2021Article
- Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data.Frontiers in genetics · 2021Article
- Validation of predicted anonymous proteins simply using Fisher's exact test.Bioinformatics advances · 2021Article
- Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage.Genome biology and evolution · 2020Article
- Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus.BMC genomics · 2020Article
- Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks.Molecular biology and evolution · 2020Article
- Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus.Scientific reports · 2019Article
- A wheat NAC interacts with an orphan protein and enhances resistance to Fusarium head blight disease.Plant biotechnology journal · 2019Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrent genome sequencing projects reveal substantial numbers of taxonomically restricted, so called orphan genes that lack homology with genes from other evolutionary lineages. However, it is not clear to what extent orphan genes are real, genomic artifacts, or represent non-coding RNAs.
resultsHere, we use a simple set of assumptions to test the nature of orphan genes. First, a sequence that is transcribed is considered a real biological entity. Second, every sequence that is supported by proteome data or shows a depletion of non-synonymous substitutions is a protein-coding gene. Using genomic, transcriptomic and proteomic data for the nematode Pristionchus pacificus, we show that between 4129-7997 (42-81 %) of predicted orphan genes are expressed and 3818-7545 (39-76 %) of orphan genes are under negative selection. In three cases that exhibited strong evolutionary constraint but lacked expression evidence in 14 RNA-seq samples, we could experimentally validate the predicted gene structures. Comparing different data sets to infer selection on orphan gene clusters, we find that the presence of a closely related genome provides the most powerful resource to robustly identify evidence of negative selection. However, even in the absence of other genomic data, the availability of paralogous sequences was enough to show negative selection in 8-10 % of orphan genes.
conclusionsOur study shows that the great majority of previously identified orphan genes in P. pacificus are indeed protein-coding genes. Even though this work represents a case study on a single species, our approach can be transferred to genomic data of other non-model organisms in order to ascertain the protein-coding nature of orphan genes.
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