Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica

Abstract

The genus Yersinia includes three human pathogens, of which Yersinia pestis is responsible for >2,000 illnesses each year. To aid in the development of detection assays and aid further phylogenetic elucidation, we sequenced and assembled the complete genomes of 32 strains (across 9 Yersinia species).

GENOME ANNOUNCEMENT

The genus Yersinia contains 11 species, with three human pathogens, Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica. Of these, Y. pestis is the most virulent, causing >2,000 global cases of plague annually, along with three global pandemics (1, 2). Y. pestis is a category A pathogen and potential biowarfare agent (3, 4), while Y. pseudotuberculosis and Y. enterocolitica cause food-borne self-limiting enteric diseases with low mortality rates (5). Recently, the list of strains for consideration in diagnostic assay development was released by the Association of Analytical Communities (AOAC) International, including strains that should be recognized (inclusivity) and ignored (exclusivity) by the assays (6). Here, we present the completed genome assemblies for 32 (see Table 1) of the 33 listed Yersinia strains (YPNN7 Y. pseudotuberculosis IB was not included due to technical issues).

TABLE 1.

List of strains included in the data set, their accession numbers, and plasmids

Strain name	AOAC	Panela	Accession no.	Size (Mb)	No. of indicated plasmid
					pPCP	pCD/pYV	pMT	Other
Y. aldovae
670-83	YPNN17	E	CP009781	4.47
Y. enterocolitica
2516-87	YPNN13	E	CP009837, CP009838	4.60		1
8081	YPNN12	E	CP009845, CP009846	4.68		1
WA	YPNN11	E	CP009366, CP009367	4.61		1
Y. frederiksenii
Y225b	YPNN15	E	CP009363, CP009364	4.55				1
Y. intermedia
Y228	YPNN16	E	CP009801	4.85
Y. kristensenii
Y231	YPNN14	E	CP009997	4.49
Y. pestis
A1122	YP12	I	CP009839–CP009841	4.67	1		1
Angola	YP7	I	CP009934– CP009937	4.67	1	1	1
Antiqua	YP3	I	CP009903– CP009906	4.88	1	1	1
CO92 pgm-	YP1	I	CP009971– CP009973	4.72		1	1
Dodson	YP15	I	CP009842– CP009844	4.77		1	1
El Dorado	YP16	I	CP009782– CP009785	4.83	1	1	1
Harbin35	YP9	I	CP009701– CP009704	4.70	1	1	1
Java9c	YP11	I	CP009992– CP009996	4.82	1	1		2
KIM5	YP2	I	CP009833– CP009836	4.78	1	1	1
Nairobi	YP8	I	CP010293, CP010294	4.47	1
Nicholisk 41	YP13	I	CP009988– CP009991	4.70	1	1	1
PBM19	YP10	I	CP009489– CP009492	4.86	1	1	1
Pestoides B	YP4	I	CP010020– CP010023	4.79	1	1	1
Pestoides F	YP5	I	CP009713– CP009715	4.72		1	1
Pestoides G	YP6	I	CP010246– CP010248	4.73		1	1
Shasta	YP14	I	CP009721– CP009724	4.83	1	1	1
Y. pseudotuberculosis
1	YPNN10	E	CP009786	4.72
EP2/+	YPNN8	E	CP009758, CP009759	4.77		1
IP32953	YPNN4	E	CP009710– CP009712	4.83		1		1
MD67	YPNN9	E	CP009757	4.72
Pa3606	YPNN6	E	CP010067– CP010069	4.83		1		1
PB1/+	YPNN3	E	CP009779, CP009780	4.76		1
YPIII	YPNN5	E	CP009792	4.68
Y. rohdei
ATCC 43380	YPNN2	E	CP009787	4.37
Y. ruckeri
YRB	YPNN1	E	CP009539	3.60

^aRefers to the AOAC listing (6) of either inclusivity (I) or exclusivity (E) strains.

^bThe plasmid in Y. frederiksenii is cryptic.

^cThe two plasmids listed as “other” for Y. pestis JAVA9 are pJARS35 and pJARS36.

Each genome was assembled using at least two data sets (specific data types and coverages are listed in the NCBI records), from Illumina (short- and/or long-insert paired data), Roche 454 (long-insert paired data), and/or PacBio long reads. The short- and long-insert paired data were assembled together in both Newbler and Velvet and computationally shredded into 1.5-kbp overlapping shreds. If the PacBio coverage was ≥100×, the data were assembled using the PacBio Hierarchical Genome Assembly Process (HGAP) (7). All data were additionally assembled in AllPaths (8). The consensus sequences from both HGAP and AllPaths were computationally shredded into 10-kbp overlapping pieces. All shreds were integrated using Phrap. Possible misassemblies were corrected and repeat regions verified using in-house scripts and manual editing in Consed (9–11). All genomes were assembled to finished-quality completion (12), and each assembly was annotated using an Ergatis-based (13) workflow, with minor manual curation.

The genome sizes averaged 4.68 ± 0.04 Mb (Table 1; the smallest is Yersinia ruckeri YRB, at 3.6 Mb, and the largest is Y. pestis Antiqua, at 4.9 Mb), with up to 4 plasmids (average, 1.6 ± 0.2). Each genome contains 3,161 to 4,419 coding sequences (average, 4,155 ± 39.9) and a G+C content of 47 to 48%. As many of the virulence genes are located on plasmids, it is interesting to note that of the 16 Y. pestis strains, only 9 had all three “traditional” plasmids (pYV/pCD1 [virulence/calcium dependence], pPCP [plasminogen activator], and pMT [murine toxin]), with one strain (Y. pestis Nairobi) containing the pPCP plasmid only.

Nucleotide sequence accession numbers.

The GenBank accession numbers for all 32 genomes are listed in Table 1.