ArticleGenome biology and evolution2018
Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 41 citations in OpenAlex.
- Pervasive genome structure heterogeneity iniScience · 2026Article
- TheeLife · 2025Article
- Gene conversion and duplication contribute to genetic variation in an outbreak ofMicrobial genomics · 2025Article
- Evolution and emergence of Mycobacterium tuberculosis.FEMS microbiology reviews · 2024Review
- Drug resistance prediction forMicrobial genomics · 2023Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- A critical evaluation ofMicrobial genomics · 2022Article
- The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis.G3 (Bethesda, Md.) · 2022Article
- Mutation bias shapes the spectrum of adaptive substitutions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis.Scientific reports · 2021Article
- ESX-1-Independent Horizontal Gene Transfer by Mycobacterium tuberculosis Complex Strains.mBio · 2021Article
- Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.eLife · 2021Article
- A new nomenclature for the livestock-associatedOpen research Europe · 2021Article
- Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization.Frontiers in veterinary science · 2021Article
- Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.PLoS pathogens · 2020Article
- GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes.Molecular biology and evolution · 2020Article
- Producing polished prokaryotic pangenomes with the Panaroo pipeline.Genome biology · 2020Article
- The devil is in the diversity: Exploring within-person evolution of Mycobacterium tuberculosis.EBioMedicine · 2020Article
- ESX/Type VII Secretion Systems-An Important Way Out for Mycobacterial Proteins.Microbiology spectrum · 2019Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
DNA acquisition via genetic recombination is considered advantageous as it has the potential to bring together beneficial mutations that emerge independently within a population. Furthermore, recombination is considered to contribute to the maintenance of genome stability by purging slightly deleterious mutations. The prevalence of recombination differs among prokaryotic species and depends on the accessibility of DNA transfer mechanisms. An exceptional example is the human pathogen Mycobacterium tuberculosis (MTB) where no clear transfer mechanisms have been so far characterized and the presence of recombination is questioned. Here, we analyze completely assembled MTB genomes in search for evidence of recombination. We find that putative recombination events are enriched in strains reconstructed by reference-guided assembly and in regions with unreliable alignments. In addition, assembly and alignment artefacts introduce phylogenetic signals that are conflicting the established MTB phylogeny. Our results reveal that the so far reported recombination events in MTB are likely to stem from methodological artefacts. We conclude that no reliable signal of recombination is observed in the currently available MTB genomes. Moreover, our study demonstrates the limitations of reference-guided genome assembly for phylogenetic reconstructions. Rigorously de novo assembled genomes of high quality are mandatory in order to distinguish true evolutionary signal from noise, in particular for low diversity species such as MTB.
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