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This article is cited in 8 scientific papers (total in 8 papers)
Bioinformatics
Short unique sequences in bacterial genomes as strain- and species-specific signatures
V. V. Panyukovab, S. S. Kiselevc, O. V. Alikinac, N. N. Nazipovaab, O. N. Ozolinecb a 142290, Institute of Mathematical Problems of Biology – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
b 142290, Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
c 142290, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
Abstract:
The paper presents a new approach for phylotyping that can be potentially used for pure cultures and for mixed bacterial populations. It is based on the use of short unique nucleotide sequences ($k$-mers) that are present in the genomes of all strains of the same species and are absent in bacterial genomes of other taxonomic groups. We show that the number $N$ of such sequences depends on the percentage bias towards $\mathrm{A/T}$ or $\mathrm{G/C}$ base pairs, increasing for genomes with approximately equal composition. We found that the largest contribution to the set of primarily unique sequences is given by $16$–$17$-mers, while sigmoidal curves reflecting the dependence of $N$ on the length of $k$-mers showed the maximum slope increment ($\Delta N/\Delta k$) for $k = 17, 18$. Unique sequences of the length $16$–$18$ bases can therefore be offered as potential markers. Comparing the sets of unique $k$-mers in the genomes of four Enterobacter strains, we estimated the level of their intraspecies stability and interspecies plasticity. As a result, we suggest discriminatory subsets as stencils for phylotyping, thereby increasing the list of genotyping markers with signatures of the new type.
Key words:
microbiomes, bacterial genomes, genotyping, unique nucleotide sequences.
Received 25.11.2017, Published 19.12.2017
Citation:
V. V. Panyukov, S. S. Kiselev, O. V. Alikina, N. N. Nazipova, O. N. Ozoline, “Short unique sequences in bacterial genomes as strain- and species-specific signatures”, Mat. Biolog. Bioinform., 12:2 (2017), 547–558
Linking options:
https://www.mathnet.ru/eng/mbb312 https://www.mathnet.ru/eng/mbb/v12/i2/p547
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