ABSTRACT
Here, we report the draft genome sequences of six Yersinia pestis subsp. microtus bv. ulegeica strains isolated from the territory of Mongolia and representing the 0.PE5 phylogroup circulating in populations of voles and picas.
GENOME ANNOUNCEMENT
Plague caused by Yersinia pestis is a zoonotic infection with an extraordinary epidemic potential. Although, genetically, Y. pestis is a monomorphic clone of its more diverse parental species, Yersinia pseudotuberculosis, there are several phylogenetic lines of the plague bacterium (1). The majority of Y. pestis strains have universal virulence against a wide range of mammals, including humans, while selective virulence is characteristic for strains from the 0.PE group circulating in populations of different Microtus spp. Such strains are highly virulent against their natural hosts and mice but have low virulence or are avirulent against guinea pigs and humans (2). The data of multilocus variable-number tandem-repeat analysis (MLVA) and clustered regularly interspaced short palindromic repeat (CRISPR) typing of Y. pestis subsp. microtus strains (3, 4) suggest that bv. ulegeica (0.PE5) strains from Mongolia represent the most recent guinea pig/human-avirulent branch of the Y. pestis phylogenetic tree. To date, only three whole-genome sequences of the strains from these ancient plague foci, which are characterized by a polymorphism of their circulating strains, have been deposited in GenBank (accession no. LIYO00000000, LIZG00000000, and LIZD00000000) (5). In this study, we sequenced eight additional strains isolated from the Sailugem (M01), Bukhen (M02), and Ochotona sp. Gurvan-Saikhan (M13) natural plague foci in Mongolia.
Whole-genome sequencing was performed using an Illumina MiSeq instrument according to the manufacturer’s instruction. DNA libraries were prepared using a Nextera DNA library preparation kit. A MiSeq v3 reagent kit was used for sequencing. For each genome, reads were assembled de novo using SPAdes v3.9 (http://cab.spbu.ru/software/spades/). Finally, we obtained from 167 to 180 contigs for each genome (Table 1). The genome sizes ranged from 4.58 to 4.69 Mb. Each genome contains 4,539 to 4,368 genes. Three strains bear three plasmids (pMT, pCD, and pPCP). Two strains lost pCD, and one strain lost pMT.
TABLE 1.
Strain-identifying information and basic statistics on assemblies and annotations
| Strain name | Focusa | SRA accession no. |
GenBank assembly accession no. |
Size (bp) |
No. of contigs |
Total genes |
Coding genes |
Plasmidb |
||
|---|---|---|---|---|---|---|---|---|---|---|
|
pMT/ pFra |
pCD/ pYV |
pPCP/ pPst |
||||||||
| SCPM-O-B-6301 (I-2231) | M01 | SRR6794312 | PVLW00000000 | 4,578,646 | 175 | 4,368 | 4,090 | − | + | + |
| SCPM-O-B-6212 (I-2238) | M01 | SRR6794311 | PVLX00000000 | 4,616,215 | 167 | 4,420 | 4,161 | + | − | + |
| SCPM-O-B-6218 (I-3190) | M13 | SRR6794314 | PVLY00000000 | 4,680,847 | 180 | 4,502 | 4,224 | + | + | + |
| SCPM-O-DNA-15 (I-2236) | M01 | SRR6794313 | PVLZ00000000 | 4,621,120 | 169 | 4,494 | 4,238 | + | − | + |
| SCPM-O-DNA-16 (I-2422 pMT+) | M02 | SRR6794316 | PVMA00000000 | 4,686,426 | 180 | 4,539 | 4,262 | + | + | + |
| SCPM-O-DNA-17 (I-2457) | M13 | SRR6794315 | PVMB00000000 | 4,679,672 | 180 | 4,535 | 4,259 | + | + | + |
Focus numbers are indicated according to reference 1.
−, not present; +, present.
Study of branches of the Y. pestis tree can give additional data about intraspecies microevolution of Y. pestis, its spread around the world, and the formation of novel natural plague foci. Perhaps new information about genome structures of representatives of different SNP types will help to answer the main question—how the enteropathogenic bacterium Yersinia pseudotuberculosis, with a fecal-oral route of transmission, gave rise to the superbug Y. pestis, the cause of infamous deadly pandemic infection.
Accession number(s).
The GenBank accession numbers for these eight genome sequences are listed in Table 1.
ACKNOWLEDGMENT
This work was supported by the Russian Science Foundation (grant 14-15-00599).
Footnotes
Citation Kislichkina AA, Bogun AG, Kadnikova LA, Maiskaya NV, Solomentsev VI, Sizova AA, Dentovskaya SV, Balakhonov SV, Anisimov AP. 2018. Six whole-genome assemblies of Yersinia pestis subsp. microtus bv. ulegeica (phylogroup 0.PE5) strains isolated from Mongolian natural plague foci. Genome Announc 6:e00536-18. https://doi.org/10.1128/genomeA.00536-18.
REFERENCES
- 1.Cui Y, Yu C, Yan Y, Li D, Li Y, Jombart T, Weinert LA, Wang Z, Guo Z, Xu L, Zhang Y, Zheng H, Qin N, Xiao X, Wu M, Wang X, Zhou D, Qi Z, Du Z, Wu H, Yang X, Cao H, Wang H, Wang J, Yao S, Rakin A, Li Y, Falush D, Balloux F, Achtman M, Song Y, Wang J, Yang R. 2013. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A 110:577–582. doi: 10.1073/pnas.1205750110. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Platonov ME, Evseeva VV, Dentovskaya SV, Anisimov AP. 2013. Molecular typing of Yersinia pestis. Mol Genet Microbiol Virol 28:41. doi: 10.3103/S0891416813020067. [DOI] [PubMed] [Google Scholar]
- 3.Platonov ME, Evseeva VV, Efremenko DV, Afanas’ev MV, Verzhutski DB, Kuznetsova IV, Shestopalov MY, Dentovskaya SV, Kulichenko AN, Balakhonov SV, Anisimov AP. 2015. Intraspecies classification of rhamnose-positive Yersinia pestis strains from natural plague foci of Mongolia. Mol Genet Microbiol Virol 30:24. doi: 10.3103/S0891416815010073. [DOI] [Google Scholar]
- 4.Platonov ME, Evseeva VV, Svetoch TE, Efremenko DV, Kuznetsova IV, Dentovskaya SV, Kulichenko AN, Anisimov AP. 2012. Phylogeography of Yersinia pestis vole strains isolated from natural foci of the Caucasus and South Caucasus. Mol Genet Microbiol Virol 27:108. doi: 10.3103/S089141681203007X. [DOI] [PubMed] [Google Scholar]
- 5.Kislichkina AA, Bogun AG, Kadnikova LA, Maiskaya NV, Platonov ME, Anisimov NV, Galkina EV, Dentovskaya SV, Anisimov AP. 2015. Nineteen whole-genome assemblies of Yersinia pestis subsp. microtus, including representatives of biovars caucasica, talassica, hissarica, altaica, xilingolensis, and ulegeica. Genome Announc 3:e01342-15. doi: 10.1128/genomeA.01342-15. [DOI] [PMC free article] [PubMed] [Google Scholar]