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On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella

BACKGROUND: To reconstruct the evolution history of DNA sequences, novel models of increasing complexity regarding the number of free parameters taken into account in the sequence evolution, as well as faster and more accurate algorithms, and statistical and computational methods, are needed. More p...

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Autores principales: Guyeux, Christophe, Al-Nuaimi, Bashar, AlKindy, Bassam, Couchot, Jean-François, Salomon, Michel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245693/
https://www.ncbi.nlm.nih.gov/pubmed/30458842
http://dx.doi.org/10.1186/s12918-018-0618-2
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author Guyeux, Christophe
Al-Nuaimi, Bashar
AlKindy, Bassam
Couchot, Jean-François
Salomon, Michel
author_facet Guyeux, Christophe
Al-Nuaimi, Bashar
AlKindy, Bassam
Couchot, Jean-François
Salomon, Michel
author_sort Guyeux, Christophe
collection PubMed
description BACKGROUND: To reconstruct the evolution history of DNA sequences, novel models of increasing complexity regarding the number of free parameters taken into account in the sequence evolution, as well as faster and more accurate algorithms, and statistical and computational methods, are needed. More particularly, as the principal forces that have led to major structural changes are genome rearrangements (such as translocations, fusions, and so on), understanding their underlying mechanisms, among other things via the ancestral genome reconstruction, are essential. In this problem, since finding the ancestral genomes that minimize the number of rearrangements in a phylogenetic tree is known to be NP-hard for three or more genomes, heuristics are commonly chosen to obtain approximations of the exact solution. The aim of this work is to show that another path is possible. RESULTS: Various algorithms and software already deal with the difficult nature of the problem of reconstruction of the ancestral genome, but they do not function with precision, in particular when indels or single nucleotide polymorphisms fall into repeated sequences. In this article, and despite the theoretical NP-hardness of the ancestral reconstruction problem, we show that an exact solution can be found in practice in various cases, encompassing organelles and some bacteria. A practical example proves that an accurate reconstruction, which also allows to highlight homoplasic events, can be obtained. This is illustrated by the reconstruction of ancestral genomes of two bacterial pathogens, belonging in Mycobacterium and Brucella genera. CONCLUSIONS: By putting together automatically reconstructed ancestral regions with handmade ones for problematic cases, we show that an accurate reconstruction of ancestors of the Brucella genus and of the Mycobacterium tuberculosis complex is possible. By doing so, we are able to investigate the evolutionary history of each pathogen by computing their common ancestors. They can be investigated extensively, by studying the gene content evolution over time, the resistance acquisition, and the impacts of mobile elements on genome plasticity.
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spelling pubmed-62456932018-11-26 On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella Guyeux, Christophe Al-Nuaimi, Bashar AlKindy, Bassam Couchot, Jean-François Salomon, Michel BMC Syst Biol Research BACKGROUND: To reconstruct the evolution history of DNA sequences, novel models of increasing complexity regarding the number of free parameters taken into account in the sequence evolution, as well as faster and more accurate algorithms, and statistical and computational methods, are needed. More particularly, as the principal forces that have led to major structural changes are genome rearrangements (such as translocations, fusions, and so on), understanding their underlying mechanisms, among other things via the ancestral genome reconstruction, are essential. In this problem, since finding the ancestral genomes that minimize the number of rearrangements in a phylogenetic tree is known to be NP-hard for three or more genomes, heuristics are commonly chosen to obtain approximations of the exact solution. The aim of this work is to show that another path is possible. RESULTS: Various algorithms and software already deal with the difficult nature of the problem of reconstruction of the ancestral genome, but they do not function with precision, in particular when indels or single nucleotide polymorphisms fall into repeated sequences. In this article, and despite the theoretical NP-hardness of the ancestral reconstruction problem, we show that an exact solution can be found in practice in various cases, encompassing organelles and some bacteria. A practical example proves that an accurate reconstruction, which also allows to highlight homoplasic events, can be obtained. This is illustrated by the reconstruction of ancestral genomes of two bacterial pathogens, belonging in Mycobacterium and Brucella genera. CONCLUSIONS: By putting together automatically reconstructed ancestral regions with handmade ones for problematic cases, we show that an accurate reconstruction of ancestors of the Brucella genus and of the Mycobacterium tuberculosis complex is possible. By doing so, we are able to investigate the evolutionary history of each pathogen by computing their common ancestors. They can be investigated extensively, by studying the gene content evolution over time, the resistance acquisition, and the impacts of mobile elements on genome plasticity. BioMed Central 2018-11-20 /pmc/articles/PMC6245693/ /pubmed/30458842 http://dx.doi.org/10.1186/s12918-018-0618-2 Text en © The Author(s) 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Guyeux, Christophe
Al-Nuaimi, Bashar
AlKindy, Bassam
Couchot, Jean-François
Salomon, Michel
On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
title On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
title_full On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
title_fullStr On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
title_full_unstemmed On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
title_short On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
title_sort on the reconstruction of the ancestral bacterial genomes in genus mycobacterium and brucella
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245693/
https://www.ncbi.nlm.nih.gov/pubmed/30458842
http://dx.doi.org/10.1186/s12918-018-0618-2
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