ArticleGenome biology and evolution2012
Quantifying homologous replacement of loci between haloarchaeal species.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 87 citations in OpenAlex.
- A roadmap to understanding and anticipating microbial gene transfer in soil communities.Microbiology and molecular biology reviews : MMBR · 2025Review
- Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.BMC genomics · 2025Article
- Net rate of lateral gene transfer in marine prokaryoplankton.The ISME journal · 2025Article
- Comparative genomics of the highly halophilic Haloferacaceae.Scientific reports · 2024Article
- Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.Genome biology and evolution · 2024Article
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- Incompatibility and Interchangeability in Molecular Evolution.Genome biology and evolution · 2023Review
- Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions.Biology direct · 2022Article
- Dead but Not Forgotten: How Extracellular DNA, Moisture, and Space Modulate the Horizontal Transfer of Extracellular Antibiotic Resistance Genes in Soil.Applied and environmental microbiology · 2022Article
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
- Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes.Molecular biology and evolution · 2021Article
- Characterization of Non-selected Intermolecular Gene Conversion in the Polyploid HaloarchaeonFrontiers in microbiology · 2021Article
- Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.Scientific reports · 2020Article
- Article
- CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria.Nature microbiology · 2019Article
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- Genotypic and Lipid Analyses of Strains From the Archaeal GenusFrontiers in microbiology · 2018Article
- Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.Genome biology and evolution · 2017Article
- Mechanisms of gene flow in archaea.Nature reviews. Microbiology · 2017Review
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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
In vitro studies of the haloarchaeal genus Haloferax have demonstrated their ability to frequently exchange DNA between species, whereas rates of homologous recombination estimated from natural populations in the genus Halorubrum are high enough to maintain random association of alleles between five loci. To quantify the effects of gene transfer and recombination of commonly held (relaxed core) genes during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history of 21 genomes representing all major groups. Using a novel algorithm and a concatenated ribosomal protein phylogeny as a reference, we created a directed horizontal genetic transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed that 90% of testable HGTs were by direct homologous replacement, rather than nonhomologous integration followed by a loss. Network analysis revealed an inverse log-linear relationship between HGT frequency and ribosomal protein evolutionary distance that is maintained across the deepest divergences in Halobacteria. We use this mathematical relationship to estimate the total transfers and amino acid substitutions delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core genes of each genome, we conservatively estimate that 11-20% of their evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer and homologous recombination of relaxed core genes between members of the class Halobacteria disrupts the coevolution of genes; however, the generation of new combinations of divergent but functionally related genes may lead to adaptive phenotypes not available through cumulative mutations and recombination within a single population.
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