ArticleGenome research2024
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome.Genome biology and evolution · 2026Article
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Integrative transcriptomic and network analysis reveals small open reading frames associated with cellular adaptive responsees and methylation-linked pathogenicity in Leptospira interrogans.Functional & integrative genomics · 2026Article
- Imported, not invented, genes prevail amongProceedings 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
- Something from nothing: The birth of new phage defense genes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 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
- 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
- Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis.Molecular biology and evolution · 2025Article
- Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Microbiome Research in Greece: A Comprehensive Bibliometric Study.Microorganisms · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course "Evolutionary and Comparative Genomics".Bioinformatics advances · 2025Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.
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