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This article is cited in 2 scientific papers (total in 2 papers)
Bioinformatics
Repeat structure in Salmonella genomes
L. A. Miroshnichenkoa, N. A. Arefievabc, Yu. P. Dzhioevb, V. D. Guseva, A. Yu. Borisenkob, S. V. Erdyneevb, Yu. S. Bukinde a Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
b Irkutsk State Medical University, Irkutsk, Russia
c Research Center for Family Health and Human Reproduction, Irkutsk, Russia
d Limnological Institute of the Siberian Branch of the RAS, Irkutsk, Russia
e Irkutsk State University, Irkutsk, Russia
Abstract:
Salmonella is a genus of gram-negative, facultative and non-spore-forming anaerobic bacteria. The genus includes two species: S. bongori and S. enterica. All Salmonella, which are pathogenic to humans and animals, belong to the species S. enterica. It includes seven subspecies, which includes more than 2500 serotypes. According to global statistics, they cause about 2.8 billion cases of diarrheal diseases annually, and the mortality rate reaches more than 300000 cases. S. enterica spp strains that have acquired multidrug resistance to antibiotics have become especially dangerous. Against the backdrop of this global problem, a detailed study of the complete genomes of various representatives of the genus Salmonella becomes relevant. Repeats play an important role in the regulation of basic genetic processes during the life cycle and evolution. The work examines various manifestations of repetition in the genomes of S. enterica. Taking into account common fragments of different genomes serves as the basis for the formation of a matrix of pairwise relative complexity, which is used in constructing a phylogenetic tree. Long repeats within individual genomes typically correspond to large individual duplications. The main attention is paid to local structural regularities, most of which are represented by tandem repeats. Of significant interest are multivalued repeats, such as tandem repeats forming a palindrome, repeats with regular substitutions or complex monomer structure.
Key words:
bacterial genome, salmonella, complex decompositions, repeats, local structural regularities, tandem repeats.
Received 13.12.2023, 19.12.2023, Published 30.12.2023
Citation:
L. A. Miroshnichenko, N. A. Arefieva, Yu. P. Dzhioev, V. D. Gusev, A. Yu. Borisenko, S. V. Erdyneev, Yu. S. Bukin, “Repeat structure in Salmonella genomes”, Mat. Biolog. Bioinform., 18:2 (2023), 602–620
Linking options:
https://www.mathnet.ru/eng/mbb536 https://www.mathnet.ru/eng/mbb/v18/i2/p602
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