Короткие Уникальные Последовательности В Бактериальных Геномах Как Штамм- И Видоспецифические Маркеры

Abstract

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 A/T or 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 (ΔN/Δk) 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.

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

“…As before, for the genomes of four Enterobacter strains, Clostridium sporogenes and Cellulomonas flavigena [44], we obtained a huge number of genus-specific k-mers with different lengths (Figure 1a, solid lines). Since the scanning was done with 1 bp resolution, most of the revealed sequences overlap, but all of them are equivalent and each can be considered as a taxonomic marker.…”

“…All the studies were based on the compact UniSeq software [44], which effectively detects unique k-mers in the tested genomes that are absent in the reference genomic database. In our case, the entire database contained 28540 nucleotide sequences of fully assembled bacterial genomes and plasmids, but the size of the reference database depended on the number of sequences belonging to the taxon of the tested genomes.…”

“…Using UniSeq in this ( Figure 1) and previous study [44], we evaluated the dependence of the number of unique k-mers on the value of k for the genomes of different taxa. Previously we observed that 17-and 18-mers gave maximum contribution to their number for the genomes of E. cloacae strains (SDM, EcWSU1, ENHKU01), E. lignolyticus SCF1, and Cl.…”

“…Previously we observed that 17-and 18-mers gave maximum contribution to their number for the genomes of E. cloacae strains (SDM, EcWSU1, ENHKU01), E. lignolyticus SCF1, and Cl. sporogenes DSM 795, while the differential plot (∆N/∆k) for marker k-mers of C. flavigena DSM 20109 had a broad peak for 18 ≤ k ≤ 21 ( Figure 1A in [44]). In this study, performed for various E. coli strains with an updated program and a significantly larger genomic database, the maximum increase in the number of strain-specific k-mers was detected in approximately the same range (18-20 n, Figure 1a).…”

“…This number is rapidly increasing in the range from 16 to 20 bp ( Figure 1a). However, for k ≥ 22 (Figure 1a and [44]), it reaches a plateau, and a further increase makes a relatively small contribution to the set of marker sequences. Therefore, we used the longest k-mer provided by the current version of UniSeq k-mers (22-mers) for taxonomic analysis.…”