Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts
Open accessAbstract
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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In contrast to M. canettii strains, DNA transfer between M. tuberculosis strains was not observed despite numerous trials, emphasizing the clonal population structure of M. tuberculosis strains.
“In contrast to M. canettii strains, DNA transfer between M. tuberculosis strains was not observed despite numerous trials (55), emphasizing the clonal population structure of M. tuberculosis strains (58,59).”
From ESX/Type VII Secretion Systems—An Important Way Out for Mycobacterial Proteins (2019) · cites this paper as [58]
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- Authors
- Godfroid, M., Dagan, T., & Kupczok, A.
- Affiliations
- Christian-Albrechts-Universität zu Kiel (DE)
- Corresponding author
- Godfroid, Maxime
- Kupczok, Anne
- Venue
- Genome Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-07-13
- Volume
- 10
- Issue
- 8
- Pages
- 1920-1926
- ISSN
- 1759-6653 (ISSN-L)
- PMC
- PMC6086087
- OpenAlex
- W2884219632
- Cited by
- 37
- References
- 55
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 8 · 2023: 4 · 2022: 5 · 2021: 7 · 2020: 5 · 2019: 3
- FWCI
- 1.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome Biology and Evolution (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- European Research Council (281357)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Mycobacterium tuberculosis, genetic recombination, phylogenetic signal, genome stability, de novo genome assembly, recombination detection
- MeSH terms
- Mycobacterium tuberculosis, Phylogeny, Recombination, Genetic, Reference Standards, Sequence Alignment, Artifacts, Genome, Bacterial
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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