ArticleGenome biology and evolution2023
Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences.
Article in Genome biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- 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
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 2025Article
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Genomic Insights intoInternational journal of molecular sciences · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Genomic Characterization ofMicroorganisms · 2024Article
- Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.Genome research · 2024Article
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria.Database : the journal of biological databases and curation · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Taxonomically restricted genes (TRGs) are unique for a defined group of organisms and may act as potential genetic determinants of lineage-specific, biological properties. Here, we explore the TRGs of highly diverse and economically important Bacillus bacteria by examining commonly used TRG identification parameters and data sources. We show the significant effects of sequence similarity thresholds, composition, and the size of the reference database in the identification process. Subsequently, we applied stringent TRG search parameters and expanded the identification procedure by incorporating an analysis of noncoding and non-syntenic regions of non-Bacillus genomes. A multiplex annotation procedure minimized the number of false-positive TRG predictions and showed nearly one-third of the alleged TRGs could be mapped to genes missed in genome annotations. We traced the putative origin of TRGs by identifying homologous, noncoding genomic regions in non-Bacillus species and detected sequence changes that could transform these regions into protein-coding genes. In addition, our analysis indicated that Bacillus TRGs represent a specific group of genes mostly showing intermediate sequence properties between genes that are conserved across multiple taxa and nonannotated peptides encoded by open reading frames.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.