ArticleGenome research2004
Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers, 1 of them a synthesis that pooled it.
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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
144 citing papers in PubMed, 1 synthesis or guideline pooled it, 263 citations in OpenAlex.
- The Landscape of Genetic Content in the Gut and Oral Human Microbiome.Cell host & microbe · 2019Pooled it
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- Sex-Specific ORFs in Marine Clams (Bivalvia: Veneridae) with Doubly Uniparental Inheritance: Exploring Their Origin and Putative Function.Marine biotechnology (New York, N.Y.) · 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
- Candidate orphan genes: Reassessing uniqueness.PloS one · 2025Article
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.Nucleic acids research · 2024Article
- Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.Genome research · 2024Article
- Origin, evolution, and maintenance of gene-strand bias in bacteria.Nucleic acids research · 2024Article
- TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria.Database : the journal of biological databases and curation · 2023Article
- On the Unknown Proteins of Eukaryotic Proteomes.Journal of molecular evolution · 2023Article
- The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth.Science advances · 2023Article
- 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
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- Whole-genome sequencing and comparative analysis of Helicobacter pylori GZ7 strain isolated from China.Folia microbiologica · 2022Article
- Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis.BMC ecology and evolution · 2022Article
- Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis.PLoS biology · 2022Article
- Factors That Affect the Rates of Adaptive and Nonadaptive Evolution at the Gene Level in Humans and Chimpanzees.Genome biology and evolution · 2022Article
84 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to gamma-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions.
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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 OpenQuestion graph.