ArticleGenome biology and evolution2009
Lateral transfer of genes and gene fragments in prokaryotes.
Article in Genome biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 92 citations in OpenAlex.
- Detecting genetic gain and loss events in terms of protein domain: Method and implementation.Heliyon · 2024Article
- Modular evolution of secretion systems and virulence plasmids in a bacterial species complex.BMC biology · 2022Article
- Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes.Molecular biology and evolution · 2021Article
- Microevolution in the major outer membrane protein OmpA ofMicrobial genomics · 2020Article
- Alignment-free inference of hierarchical and reticulate phylogenomic relationships.Briefings in bioinformatics · 2019Review
- Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity.BMC genomics · 2018Article
- Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems.Biophysical journal · 2017Article
- Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.Frontiers in microbiology · 2017Article
- Exploring lateral genetic transfer among microbial genomes using TF-IDF.Scientific reports · 2016Article
- Horizontally transferred genes cluster spatially and metabolically.Biology direct · 2015Article
- Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.BMC genomics · 2015Article
- Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.Frontiers in microbiology · 2015Article
- Superoxide dismutases and superoxide reductases.Chemical reviews · 2014Review
- Interactions in the microbiome: communities of organisms and communities of genes.FEMS microbiology reviews · 2014Review
- Clustering evolving proteins into homologous families.BMC bioinformatics · 2013Article
- Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes.Genome biology · 2013Article
- Next-generation phylogenomics.Biology direct · 2013Article
- rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.Evolutionary bioinformatics online · 2013Article
- Various pathways leading to the acquisition of antibiotic resistance by natural transformation.Mobile genetic elements · 2012Article
- Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.Open biology · 2012Article
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Lateral genetic transfer (LGT) involves the movement of genetic material from one lineage into another and its subsequent incorporation into the new host genome via genetic recombination. Studies in individual taxa have indicated lateral origins for stretches of DNA of greatly varying length, from a few nucleotides to chromosome size. Here we analyze 1,462 sets of single-copy, putatively orthologous genes from 144 fully sequenced prokaryote genomes, asking to what extent complete genes and fragments of genes have been transferred and recombined in LGT. Using a rigorous phylogenetic approach, we find evidence for LGT in at least 476 (32.6%) of these 1,462 gene sets: 286 (19.6%) clearly show one or more "observable recombination breakpoints" within the boundaries of the open reading frame, while a further 190 (13.0%) yield trees that are topologically incongruent with the reference tree but do not contain a recombination breakpoint within the open reading frame. We refer to these gene sets as observable recombination breakpoint positive (ORB(+)) and negative (ORB(-)) respectively. The latter are prima facie instances of lateral transfer of an entire gene or beyond. We observe little functional bias between ORB(+) and ORB(-) gene sets, but find that incorporation of entire genes is potentially more frequent in pathogens than in nonpathogens. As ORB(+) gene sets are about 50% more common than ORB(-) sets in our data, the transfer of gene fragments has been relatively frequent, and the frequency of LGT may have been systematically underestimated in phylogenetic studies.
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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.