article published yes Alexey Zabelkin author Yulia Yakovleva author Olga Bochkareva author C4558D3C-6102-11E9-A62E-F418E66974250000-0003-1006-6639 Nikita Alexeev author FyKo department ISTplus - Postdoctoral Fellowships project 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. https://research-explorer.ista.ac.at/download/10927/10930/2022_Bioinformatics_Zabelkin.pdf application/pdfno Oxford University Press2022 eng 1367-4803 1460-2059 00074338010000810.1093/bioinformatics/btab691 382357-363 https://github.com/ctlab/parallel-rearrangements A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel REarrangements and BReaks identification toolkit,” <i>Bioinformatics</i>, vol. 38, no. 2. Oxford University Press, pp. 357–363, 2022. Zabelkin, A., Yakovleva, Y., Bochkareva, O., &#38; Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>. Oxford University Press. <a href="https://doi.org/10.1093/bioinformatics/btab691">https://doi.org/10.1093/bioinformatics/btab691</a> Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>, vol. 38, no. 2, Oxford University Press, 2022, pp. 357–63, doi:<a href="https://doi.org/10.1093/bioinformatics/btab691">10.1093/bioinformatics/btab691</a>. Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363. Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>. 2022;38(2):357-363. doi:<a href="https://doi.org/10.1093/bioinformatics/btab691">10.1093/bioinformatics/btab691</a> Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>. Oxford University Press, 2022. <a href="https://doi.org/10.1093/bioinformatics/btab691">https://doi.org/10.1093/bioinformatics/btab691</a>. A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022) 357–363. 109272022-03-27T22:01:46Z2025-05-14T11:05:09Z