Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts.

Godfroid, Maxime, Dagan, Tal, Kupczok, Anneke and Hershberg, Ruth (2018) Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts. Open Access Genome Biology and Evolution, 10 (8). pp. 1920-1926. DOI 10.1093/gbe/evy143.

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Supplementary data:

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.

Document Type: Article
Keywords: phylogeny, recombination, Mycobacterium tuberculosis, comparative genomics, assembly, alignment
Research affiliation: Kiel University > Kiel Marine Science
OceanRep > The Future Ocean - Cluster of Excellence
Kiel University
Refereed: Yes
Open Access Journal?: Yes
DOI etc.: 10.1093/gbe/evy143
ISSN: 1759-6653
Projects: Future Ocean
Date Deposited: 10 Dec 2018 11:02
Last Modified: 27 Mar 2019 11:11
URI: http://oceanrep.geomar.de/id/eprint/44905

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