ABSTRACT
We report here the draft genome sequences of nine Yersinia pestis subsp. microtus bv. Altaica strains isolated from the Altai Mountain plague focus (no. 36), which represent the 0.PE4 phylogroup circulating in populations of Mongolian pika (Ochotona pallasi).
GENOME ANNOUNCEMENT
The plague is a zoonotic infection caused by the Gram-negative bacterium Yersinia pestis, which is occasionally transmitted to humans from infected rodents through the bites of infected fleas. The majority of the natural plague foci are not geographically connected, resulting in considerable ecological differences needed for Y. pestis to survive and be transmitted in these different environments. Adaptation to dissimilar living conditions led to the formation of considerable diversity in genotypes and phenotypes among Y. pestis isolates from different natural foci.
The Altai Mountain natural plague focus (no. 36) is the Russian part of the Sailugem natural plague focus located in the northwest of Mongolia (1). The main components of this natural focus are populations of Y. pestis 0.PE4 phylogroup strains belonging to Y. pestis subsp. microtus and characterized by high virulence to their main host (Ochotona pallasi) and laboratory mice but almost always avirulence or weak virulence for guinea pigs and humans (2). Although this plague focus is characterized by permanent epizootic activity, its epidemic potential is low, and there were no registered cases of the disease in people (3).
DNA samples were extracted using conventional SDS lysis and phenol-chloroform extraction methods.
Whole-genome sequencing was performed using an Illumina MiSeq instrument according to the manufacturer’s instruction. DNA libraries were prepared using the Nextera DNA laboratory preparation kit. A MiSeq reagent kit v3 was used for sequencing. For each genome, reads were assembled de novo using SPAdes v.3.8.1 (http://cab.spbu.ru/software/spades/). Finally, we obtained from 167 to 211 contigs for each genome (Table 1). The genome sizes ranged from 4.61 to 4.65 Mb. Each genome contains 4,255 to 4,511 genes. All strains except one have three plasmids (pMT, pCD, and pPCP). Strain I-3442 does not carry plasmid pPCP, but the other two plasmids are present.
TABLE 1 .
Strain-identifying information and basic statistics on assemblies and annotations
| Strain name |
Alternative strain name |
SRA accession no. (raw data) |
GenBank accession no. |
Size (bp) | No. of contigs |
No. of genes |
Plasmida |
|||
|---|---|---|---|---|---|---|---|---|---|---|
| Total | Coding | pMT/pFra | pCD/pYV | pPCP/pPst | ||||||
| I-3442 | SCPM-O-DNA-01 | SRR4017182 | NHYH00000000 | 4,641,984 | 181 | 4,449 | 4,205 | + | + | − |
| I-3443 | SCPM-O-DNA-02 | SRR4017184 | MIED00000000 | 4,646,108 | 167 | 4,255 | 4,054 | + | + | + |
| I-3446 | SCPM-O-DNA-03 | SRR4017191 | NHYI00000000 | 4,651,412 | 211 | 4,477 | 4,232 | + | + | + |
| I-3447 | SCPM-O-DNA-04 | SRR4017192 | MIEE00000000 | 4,646,075 | 167 | 4,268 | 4,053 | + | + | + |
| I-3515 | SCPM-O-DNA-05 | SRR4017193 | NHYJ00000000 | 4,650,263 | 187 | 4,465 | 4,225 | + | + | + |
| I-3516 | SCPM-O-DNA-06 | SRR4017195 | NHMW00000000 | 4,647,570 | 172 | 4,487 | 4,252 | + | + | + |
| I-3517 | SCPM-O-DNA-07 | SRR4017197 | NHMX00000000 | 4,612,130 | 182 | 4,469 | 4,241 | + | + | + |
| I-3518 | SCPM-O-DNA-08 | SRR4017214 | NHMY00000000 | 4,652,539 | 198 | 4,511 | 4,270 | + | + | + |
| I-3519 | SCPM-O-DNA-09 | SRR4017215 | NHMZ00000000 | 4,650,126 | 179 | 4,475 | 4,251 | + | + | + |
−, not present; +, present.
A detailed report of a full comparative genomic analysis will be included in a future publication.
Accession number(s).
The GenBank accession numbers for these nine genome sequences are listed in Table 1.
ACKNOWLEDGMENTS
This work was supported by the Russian Science Foundation (grant 14-15-00599).
The bacterial strains are stored in the Irkutsk Antiplague Research Institute of Siberia and the Far East (Irkutsk, Russian Federation).
Footnotes
Citation Kislichkina AA, Bogun AG, Kadnikova LA, Maiskaya NV, Solomentsev VI, Dentovskaya SV, Balakhonov SV, Anisimov AP. 2018. Nine whole-genome assemblies of Yersinia pestis subsp. microtus bv. Altaica strains isolated from the Altai Mountain natural plague focus (no. 36) in Russia. Genome Announc 6:e01440-17. https://doi.org/10.1128/genomeA.01440-17.
REFERENCES
- 1.Anisimov AP, Lindler LE, Pier GB. 2004. Intraspecific diversity of Yersinia pestis. Clin Microbiol Rev 17:434–464. doi: 10.1128/CMR.17.2.434-464.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.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 30:24–29. doi: 10.3103/S0891416815010073. [DOI] [Google Scholar]
- 3.Onishchenko GG, Kutyrev VV. 2004. Natural plague foci in the territory of Caucasus, Caspian-Sea Region, Central Asia and Siberia. Medicina, Moscow, Russia: (In Russian.) [Google Scholar]