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PaReBrick: PArallel REarrangements and BReaks identification toolkit
MOTIVATION: High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, provi...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723149/ https://www.ncbi.nlm.nih.gov/pubmed/34601581 http://dx.doi.org/10.1093/bioinformatics/btab691 |
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author | Zabelkin, Alexey Yakovleva, Yulia Bochkareva, Olga Alexeev, Nikita |
author_facet | Zabelkin, Alexey Yakovleva, Yulia Bochkareva, Olga Alexeev, Nikita |
author_sort | Zabelkin, Alexey |
collection | PubMed |
description | MOTIVATION: High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. RESULTS: Here, we define the term ‘parallel rearrangements’ as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. AVAILABILITY AND IMPLEMENTATION: PaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-8723149 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87231492022-01-05 PaReBrick: PArallel REarrangements and BReaks identification toolkit Zabelkin, Alexey Yakovleva, Yulia Bochkareva, Olga Alexeev, Nikita Bioinformatics Original Paper MOTIVATION: High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. RESULTS: Here, we define the term ‘parallel rearrangements’ as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. AVAILABILITY AND IMPLEMENTATION: PaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-10-02 /pmc/articles/PMC8723149/ /pubmed/34601581 http://dx.doi.org/10.1093/bioinformatics/btab691 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Paper Zabelkin, Alexey Yakovleva, Yulia Bochkareva, Olga Alexeev, Nikita PaReBrick: PArallel REarrangements and BReaks identification toolkit |
title | PaReBrick: PArallel REarrangements and BReaks identification toolkit |
title_full | PaReBrick: PArallel REarrangements and BReaks identification toolkit |
title_fullStr | PaReBrick: PArallel REarrangements and BReaks identification toolkit |
title_full_unstemmed | PaReBrick: PArallel REarrangements and BReaks identification toolkit |
title_short | PaReBrick: PArallel REarrangements and BReaks identification toolkit |
title_sort | parebrick: parallel rearrangements and breaks identification toolkit |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723149/ https://www.ncbi.nlm.nih.gov/pubmed/34601581 http://dx.doi.org/10.1093/bioinformatics/btab691 |
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