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Genome rearrangements and phylogeny reconstruction in Yersinia pestis

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleot...

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Autores principales: Bochkareva, Olga O., Dranenko, Natalia O., Ocheredko, Elena S., Kanevsky, German M., Lozinsky, Yaroslav N., Khalaycheva, Vera A., Artamonova, Irena I., Gelfand, Mikhail S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5877447/
https://www.ncbi.nlm.nih.gov/pubmed/29607260
http://dx.doi.org/10.7717/peerj.4545
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author Bochkareva, Olga O.
Dranenko, Natalia O.
Ocheredko, Elena S.
Kanevsky, German M.
Lozinsky, Yaroslav N.
Khalaycheva, Vera A.
Artamonova, Irena I.
Gelfand, Mikhail S.
author_facet Bochkareva, Olga O.
Dranenko, Natalia O.
Ocheredko, Elena S.
Kanevsky, German M.
Lozinsky, Yaroslav N.
Khalaycheva, Vera A.
Artamonova, Irena I.
Gelfand, Mikhail S.
author_sort Bochkareva, Olga O.
collection PubMed
description Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.
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spelling pubmed-58774472018-03-30 Genome rearrangements and phylogeny reconstruction in Yersinia pestis Bochkareva, Olga O. Dranenko, Natalia O. Ocheredko, Elena S. Kanevsky, German M. Lozinsky, Yaroslav N. Khalaycheva, Vera A. Artamonova, Irena I. Gelfand, Mikhail S. PeerJ Bioinformatics Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content. PeerJ Inc. 2018-03-27 /pmc/articles/PMC5877447/ /pubmed/29607260 http://dx.doi.org/10.7717/peerj.4545 Text en ©2018 Bochkareva et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Bochkareva, Olga O.
Dranenko, Natalia O.
Ocheredko, Elena S.
Kanevsky, German M.
Lozinsky, Yaroslav N.
Khalaycheva, Vera A.
Artamonova, Irena I.
Gelfand, Mikhail S.
Genome rearrangements and phylogeny reconstruction in Yersinia pestis
title Genome rearrangements and phylogeny reconstruction in Yersinia pestis
title_full Genome rearrangements and phylogeny reconstruction in Yersinia pestis
title_fullStr Genome rearrangements and phylogeny reconstruction in Yersinia pestis
title_full_unstemmed Genome rearrangements and phylogeny reconstruction in Yersinia pestis
title_short Genome rearrangements and phylogeny reconstruction in Yersinia pestis
title_sort genome rearrangements and phylogeny reconstruction in yersinia pestis
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5877447/
https://www.ncbi.nlm.nih.gov/pubmed/29607260
http://dx.doi.org/10.7717/peerj.4545
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