The study of potential recombination events in the protein-coding regions of CRISPR-Cas loci in the genomes of different Salmonella enterica serovariants using in silico methods

Background . The study of recombination processes in the CRISPR-Cas loci of Salmonella enterica can help investigate the fundamental evolutionary mechanisms of the CRISPR-Cas system to better understand the acquisition of phage resistance. The aim of the study . To investigate the recombination processes in the proteincoding regions of CRISPR-Cas loci in the genomes of Salmonella enterica serovars Enteritidis, Infantis, and Typhimurium using in silico methods. Materials and methods . The genomic sequences of the Salmonella serovars Enteritidis, Infantis, and Typhimurium were downloaded from the NCBI GenBank database. The coding sequences of cas genes were extracted from the genomes and aligned according to codon position. Recombination events were identified in the resulting alignment using multiple algorithms. Verification of recombination events was performed. Results . A total of 7683 potential recombination events were identified. Among these, 810 (10.54 %) were verified, and 45 (0.59 %) were recognized as results of convergent evolution. Recombination events are detected more frequently between strains belonging to different serovariants than between those of the same serovariant. All serovariants can recombine with each other; however, recombination primarily occurs between Enteritidis and Infantis strains, as well as between Typhimurium and Infantis strains. Infantis and Typhimurium serovariants also exhibit recombination within themselves. No recombination events were found between strains of the Enteritidis serovariant. The events of convergent adaptive evolution were mainly found in the effector module genes: cas5, cas6, cas7. Conclusion . It has been shown that homologous recombination often occurs in the S. enterica genome in the region of the cas genes. Bioinformatic algorithms detect more recombination events between evolutionarily more distant strains, which are inconsistent with known in vitro studies.