ArticlePLoS computational biology2008
The emergence and fate of horizontally acquired genes in Escherichia coli.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.Microbiome · 2025Article
- Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility.Nucleic acids research · 2024Article
- Horizontal gene transfer and adaptive evolution in bacteria.Nature reviews. Microbiology · 2022Review
- Article
- CCA-Addition Gone Wild: Unusual Occurrence and Phylogeny of Four Different tRNA Nucleotidyltransferases in Acanthamoeba castellanii.Molecular biology and evolution · 2021Article
- Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage.The ISME journal · 2021Article
- Characterization of capsule genes in non-pathogenic Neisseria species.Microbial genomics · 2018Article
- ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements.BMC bioinformatics · 2018Article
- Genetic Competence Drives Genome Diversity in Bacillus subtilis.Genome biology and evolution · 2018Article
- Prediction of Horizontally and Widely Transferred Genes in Prokaryotes.Evolutionary bioinformatics online · 2018Article
- The chromosomal organization of horizontal gene transfer in bacteria.Nature communications · 2017Article
- Article
- Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species.Frontiers in microbiology · 2017Article
- Evolutionary assembly patterns of prokaryotic genomes.Genome research · 2016Article
- Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.BMC evolutionary biology · 2015Article
- The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.BMC evolutionary biology · 2015Article
- An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli.BMC genomics · 2014Article
- Article
- Selection on horizontally transferred and duplicated genes in sinorhizobium (ensifer), the root-nodule symbionts of medicago.Genome biology and evolution · 2014Article
- Article
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3 authors.
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Abstract
Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates.
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