Zabelkin, Alexey; Yakovleva, Yulia; Bochkareva, OlgaISTA ; Alexeev, Nikita
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.
The authors thank the 2020 student class of the Bioinformatics Institute, who used the first versions of the tool and provided many valuable suggestions to improve usability. They also thank Louisa Gonzalez Somermeyer for manuscript proofreading This work was supported by the National Center for Cognitive Research of ITMO University and JetBrains Research [to A.Z and N.A.]; and the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie [754411 to O.B.]. PaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements.
Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 2022;38(2):357-363. doi:10.1093/bioinformatics/btab691
Zabelkin, A., Yakovleva, Y., Bochkareva, O., & Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btab691
Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” Bioinformatics. Oxford Academic, 2022. https://doi.org/10.1093/bioinformatics/btab691.
A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel REarrangements and BReaks identification toolkit,” Bioinformatics, vol. 38, no. 2. Oxford Academic, pp. 357–363, 2022.
Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.
Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” Bioinformatics, vol. 38, no. 2, Oxford Academic, 2022, pp. 357–63, doi:10.1093/bioinformatics/btab691.
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