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.

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