Genome rearrangements and phylogeny reconstruction in Yersinia pestis
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics, Mathematical Biology
- Keywords
- phylogeny reconstruction, bacteria evolution, genome rearrangements
- Copyright
- © 2017 Bochkareva et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, 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 Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ Preprints 5:e3223v1 https://doi.org/10.7287/peerj.preprints.3223v1
Abstract
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 the evolutionary history of genome rearrangements in Y. pestis. We also reconciled phylogenetic trees for each of the three CRISPR-loci to obtain an integrated scenario of the CRISPR-cassette evolution. We detected numerous parallel inversions and gain/loss events by the analysis of contradictions between the obtained evolutionary trees. We also tested the hypotheses that large within-replichore inversions tend to be balanced by subsequent reversal events and that the core genes less frequently switch the chain by inversions. Both predictions were not confirmed.
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.
Author Comment
This is a submission to PeerJ for review.