ArticlemSystems
Orphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Adaptation without Dominance in Pseudomonas syringae Pathovars.Microbial ecology · 2025Article
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- Metagenomic analysis of heavy water-adapted bacterial communities.Microbial genomics · 2025Article
- Identification of a Highly VirulentPlants (Basel, Switzerland) · 2025Article
- Candidate orphan genes: Reassessing uniqueness.PloS one · 2025Article
- Metabolites: a converging node of host and microbe to explain meta-organism.Frontiers in microbiology · 2024Review
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences.Genome biology and evolution · 2023Article
- Critical assessment of pan-genomic analysis of metagenome-assembled genomes.Briefings in bioinformatics · 2022Article
- Polyphenol Utilization Proteins in the Human Gut Microbiome.Applied and environmental microbiology · 2022Article
- Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity.Journal of fungi (Basel, Switzerland) · 2021Article
- Validation of predicted anonymous proteins simply using Fisher's exact test.Bioinformatics advances · 2021Article
- Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes.Frontiers in plant science · 2021Article
- Cadmium stress triggers significant metabolic reprogramming inComputational and structural biotechnology journal · 2021Article
- Distinct but Intertwined Evolutionary Histories of Multiple Salmonella enterica Subspecies.mSystems · 2020Article
- Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches.mSystems · 2019Article
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Authors and funding
3 authors.
Funding
Abstract
Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple pathogenic genomes; and (iv) NS-ORFans (NP), which are found in multiple nonpathogenic genomes. Within the same genus, pathogens do not always have more genes, more ORFans, or more pathogenicity-related genes (PRGs)-including prophages, pathogenicity islands (PAIs), virulence factors (VFs), and horizontal gene transfers (HGTs)-than nonpathogens. Interestingly, in pathogens of the nine genera, the percentages of PS-ORFans are consistently higher than those of SS-ORFans, which is not true in nonpathogens. Similarly, in pathogens of the nine genera, the percentages of PS-ORFans matching the four types of PRGs are also always higher than those of SS-ORFans, but this is not true in nonpathogens. All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity.
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