---
_id: '8265'
abstract:
- lang: eng
  text: 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.
article_number: e4545
article_processing_charge: No
article_type: original
author:
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Natalia O.
  full_name: Dranenko, Natalia O.
  last_name: Dranenko
- first_name: Elena S.
  full_name: Ocheredko, Elena S.
  last_name: Ocheredko
- first_name: German M.
  full_name: Kanevsky, German M.
  last_name: Kanevsky
- first_name: Yaroslav N.
  full_name: Lozinsky, Yaroslav N.
  last_name: Lozinsky
- first_name: Vera A.
  full_name: Khalaycheva, Vera A.
  last_name: Khalaycheva
- first_name: Irena I.
  full_name: Artamonova, Irena I.
  last_name: Artamonova
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny
    reconstruction in Yersinia pestis. <i>PeerJ</i>. 2018;6. doi:<a href="https://doi.org/10.7717/peerj.4545">10.7717/peerj.4545</a>
  apa: Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky,
    Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and
    phylogeny reconstruction in Yersinia pestis. <i>PeerJ</i>. PeerJ. <a href="https://doi.org/10.7717/peerj.4545">https://doi.org/10.7717/peerj.4545</a>
  chicago: Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky,
    Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S.
    Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.”
    <i>PeerJ</i>. PeerJ, 2018. <a href="https://doi.org/10.7717/peerj.4545">https://doi.org/10.7717/peerj.4545</a>.
  ieee: O. Bochkareva <i>et al.</i>, “Genome rearrangements and phylogeny reconstruction
    in Yersinia pestis,” <i>PeerJ</i>, vol. 6. PeerJ, 2018.
  ista: Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva
    VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction
    in Yersinia pestis. PeerJ. 6, e4545.
  mla: Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction
    in Yersinia Pestis.” <i>PeerJ</i>, vol. 6, e4545, PeerJ, 2018, doi:<a href="https://doi.org/10.7717/peerj.4545">10.7717/peerj.4545</a>.
  short: O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky,
    V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).
date_created: 2020-08-15T11:08:23Z
date_published: 2018-03-27T00:00:00Z
date_updated: 2023-02-23T13:28:57Z
day: '27'
doi: 10.7717/peerj.4545
extern: '1'
external_id:
  pmid:
  - '29607260'
intvolume: '         6'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.7717/peerj.4545
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PeerJ
publication_identifier:
  issn:
  - 2167-8359
publication_status: published
publisher: PeerJ
quality_controlled: '1'
status: public
title: Genome rearrangements and phylogeny reconstruction in Yersinia pestis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2018'
...