ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2015 Feb 13

PMID 25675341

Citations 480

Authors

Xavier Didelot

Daniel J Wilson

Affiliations

Soon will be listed here.

Abstract

Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/.

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References

Stamatakis A . RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006; 22(21):2688-90. DOI: 10.1093/bioinformatics/btl446. View

Milkman R, Bridges M . Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics. 1990; 126(3):505-17. PMC: 1204208. DOI: 10.1093/genetics/126.3.505. View

Ochman H, Lawrence J, Groisman E . Lateral gene transfer and the nature of bacterial innovation. Nature. 2000; 405(6784):299-304. DOI: 10.1038/35012500. View

Sheppard S, McCarthy N, Falush D, Maiden M . Convergence of Campylobacter species: implications for bacterial evolution. Science. 2008; 320(5873):237-9. DOI: 10.1126/science.1155532. View

Schierup M, Hein J . Recombination and the molecular clock. Mol Biol Evol. 2000; 17(10):1578-9. DOI: 10.1093/oxfordjournals.molbev.a026256. View

Didelot X, Lawson D, Darling A, Falush D . Inference of homologous recombination in bacteria using whole-genome sequences. Genetics. 2010; 186(4):1435-49. PMC: 2998322. DOI: 10.1534/genetics.110.120121. View

Wiuf C, Hein J . The coalescent with gene conversion. Genetics. 2000; 155(1):451-62. PMC: 1461050. DOI: 10.1093/genetics/155.1.451. View

Jolley K, Wilson D, Kriz P, McVean G, Maiden M . The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis. Mol Biol Evol. 2004; 22(3):562-9. DOI: 10.1093/molbev/msi041. View

Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, Hohna S . MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012; 61(3):539-42. PMC: 3329765. DOI: 10.1093/sysbio/sys029. View

10.

Walker T, Ip C, Harrell R, Evans J, Kapatai G, Dedicoat M . Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2012; 13(2):137-46. PMC: 3556524. DOI: 10.1016/S1473-3099(12)70277-3. View

11.

Didelot X, Lawson D, Falush D . SimMLST: simulation of multi-locus sequence typing data under a neutral model. Bioinformatics. 2009; 25(11):1442-4. DOI: 10.1093/bioinformatics/btp145. View

12.

Maiden M, Jansen van Rensburg M, Bray J, Earle S, Ford S, Jolley K . MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013; 11(10):728-36. PMC: 3980634. DOI: 10.1038/nrmicro3093. View

13.

Jolley K, Bliss C, Bennett J, Bratcher H, Brehony C, Colles F . Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (Reading). 2012; 158(Pt 4):1005-1015. PMC: 3492749. DOI: 10.1099/mic.0.055459-0. View

14.

Laabei M, Recker M, Rudkin J, Aldeljawi M, Gulay Z, Sloan T . Predicting the virulence of MRSA from its genome sequence. Genome Res. 2014; 24(5):839-49. PMC: 4009613. DOI: 10.1101/gr.165415.113. View

15.

Pupko T, Peer I, Shamir R, Graur D . A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol. 2000; 17(6):890-6. DOI: 10.1093/oxfordjournals.molbev.a026369. View

16.

Didelot X, Achtman M, Parkhill J, Thomson N, Falush D . A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?. Genome Res. 2006; 17(1):61-8. PMC: 1716267. DOI: 10.1101/gr.5512906. View

17.

Harris S, Feil E, Holden M, Quail M, Nickerson E, Chantratita N . Evolution of MRSA during hospital transmission and intercontinental spread. Science. 2010; 327(5964):469-74. PMC: 2821690. DOI: 10.1126/science.1182395. View

18.

Chewapreecha C, Harris S, Croucher N, Turner C, Marttinen P, Cheng L . Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014; 46(3):305-309. PMC: 3970364. DOI: 10.1038/ng.2895. View

19.

Eyre D, Golubchik T, Gordon N, Bowden R, Piazza P, Batty E . A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open. 2012; 2(3). PMC: 3378946. DOI: 10.1136/bmjopen-2012-001124. View

20.

McVean G, Awadalla P, Fearnhead P . A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics. 2002; 160(3):1231-41. PMC: 1462015. DOI: 10.1093/genetics/160.3.1231. View