Large-scale detection of recombination in nucleotide sequences

Restriction-modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.homologous recombination | horizontal gene transfer | bacterial evolution

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“…HR is notoriously difficult to quantify accurately (24). We used five different programs to detect HR in the core genome (SI Methods).…”

Section: Resultsmentioning

confidence: 99%

Regulation of genetic flux between bacteria by restriction–modification systems

Oliveira

Touchon

Rocha

2016

Proc. Natl. Acad. Sci. U.S.A.

144

150

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“…We applied a two-phase strategy (17) to detect recombination in each of the 1,354 gene sets, the first phase involving three statistical tests for inferring phylogenetic discrepancies and the second involving a Bayesian approach to more-accurately identify ORBs (see Materials and Methods). Of the 1,354 gene sets, we found 401 (29.6%) that show evidence of within-gene recombination (i.e., sets containing one or more ORBs) after first-phase screening for phylogenetic discrepancies.…”

Section: Resultsmentioning

confidence: 99%

“…We used a two-phase strategy (17) for detecting recombination within each gene set. Three P value statistics-the maximal chi-squared value (71), the neighbor similarity score (52), and the pairwise homoplasy index, as implemented in PhiPack (12)-were first used to detect evidence of recombination events within the sequence sets based on discrepancies in phylogenetic signals.…”

Section: ϫ3mentioning

confidence: 99%

Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements

2011

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The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13 Staphylococcus genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within S. aureus appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.Staphylococci are nonmotile but invasive Gram-positive bacteria that are associated with various pus-forming diseases in humans and other animals. The most prominent pathogenic species in the genus is Staphylococcus aureus, of which various strains colonize the nasal passages and skin in humans, causing illnesses that range from minor skin lesions or infections to life-threatening diseases, e.g., meningitis, septicemia (bacteremia), and toxic shock syndrome (55,67,94). The other species of Staphylococcus, although lacking genes that encode virulence factors and toxins, are opportunistic pathogens for immunocompromised patients (2, 74, 82).One of the major problems in the prognosis of staphylococcal infections is the progressive development of resistance in the Staphylococcus species to multiple antibiotics (14), e.g., methicillin (36, 102) and vancomycin (23, 84), which has, as in other pathogenic bacteria, been attributed to the susceptibility of the organisms to genetic transfer (22, 83). Lateral genetic transfer (LGT) occurs when the organisms acquire exogenous genetic material that encodes antibiotic resistance (6, 105), and this material becomes established in the lineage, whether by recombination into the genome or, potentially less stably, on an extrachromosomal genetic element (31, 86). In Staphylococcus, transfer of genetic material has been shown to be mediated by phage transduction and conjugative transfer (19,62,79).Although a number of studies have examined the frequency of LGT in prokaryotes us...

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“…While, reassortment and recombination are biologically very different processes they result in similar exchanges of genetic material; reassortment can be viewed as a form of rearrangment, where the rearrangement breakpoints only occur at a small set of locations. In the general rearrangement detection problem, the multitude of possible breakpoint locations is the focus of most methods [2] and typically the candidate parental sequences and putative recombinants are part of the input [12,16]. In the reassortment detection problem, in contrast, the reassorted taxa are the subject of interest and specifically here we wish to recover all discernible signals of reassortment events and the associated sets of resulting taxa.…”

Section: Introductionmentioning

confidence: 99%

“…[12,2,16]). While, reassortment and recombination are biologically very different processes they result in similar exchanges of genetic material; reassortment can be viewed as a form of rearrangment, where the rearrangement breakpoints only occur at a small set of locations.…”

Section: Introductionmentioning

confidence: 99%

Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques

Nagarajan

Kingsford

2008

2008 IEEE International Conference on Bioinformatics and Biomedicine

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The evolutionary histories of viral genomes have received significant recent attention due to their importance in understanding virulence and the corresponding ramifications to public health. We present a novel framework to detect reassortment events in influenza based on the comparison of two distributions of phylogenetic trees, rather than a pair of, possibly unreliable, consensus trees. We show how to detect all high-probability inconsistencies between two distributions of trees by enumerating maximal bicliques within a defined incompatibility graph. In the process, we give the first quadratic delay algorithm for enumerating maximal bicliques within general bipartite graphs. We demonstrate the utility of our approach by applying it to several sets of influenza genomes (both human-and avianhosted) and successfully identify all known reassortment events and a few novel candidate reassortments. In addition, on simulated datasets, our approach correctly finds implanted reassortments and rarely detects reassortments where none were introduced.

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Large-scale detection of recombination in nucleotide sequences

Cited by 14 publications

References 11 publications

Regulation of genetic flux between bacteria by restriction–modification systems

Regulation of genetic flux between bacteria by restriction–modification systems

Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements

Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques

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