Molecular and genomic features of Mycobacterium bovis strain 1595 isolated from Korean cattle

Narae Kim; Yunho Jang; Jin Kyoung Kim; Soyoon Ryoo; Ka Hee Kwon; Miso Kim; Shin Seok Kang; Hyeon Seop Byeon; Hee Soo Lee; Young-Hee Lim; Jae-Myung Kim

doi:10.4142/jvs.2017.18.S1.333

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Kim, Jang, Kim, Ryoo, Kwon, Kim, Kang, Byeon, Lee, Lim, and Kim: Molecular and genomic features of Mycobacterium bovis strain 1595 isolated from Korean cattle

Original Article

J Vet Sci 2017; 18(S1): 333-341.

Published online: 4 December 2017

DOI: https://doi.org/10.4142/jvs.2017.18.S1.333

Molecular and genomic features of Mycobacterium bovis strain 1595 isolated from Korean cattle

Narae Kim^1,², Yunho Jang¹, Jin Kyoung Kim¹, Soyoon Ryoo¹, Ka Hee Kwon¹, Miso Kim¹, Shin Seok Kang⁴, Hyeon Seop Byeon⁴, Hee Soo Lee¹, Young-Hee Lim³, Jae-Myung Kim^1,^*

¹Bacterial Disease Division, Animal and Plant Quarantine Agency, Anyang 14089, Korea

²Department of Integrated Biomedical and Life Science, College of Health Science, Korea University, Seoul 02841, Korea

³Department of Public Health Science (Brain Korea 21 PLUS Program), Graduate School, Korea University, Seoul 02841, Korea

⁴Chungcheongbukdo Veterinary Service, Chungju 27492, Korea

^*Corresponding authors: Tel: +82-31-467-1823; Fax: +82-31-467-1778; E-mails: kimjm88@korea.kr (JM Kim), yhlim@korea.ac.kr (YH Lim)

Received 11 July 2016 Revised 11 October 2016 Accepted 2 January 2017

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The aim of this study was to investigate the molecular characteristics and to conduct a comparative genomic analysis of Mycobacterium (M.) bovis strain 1595 isolated from a native Korean cow. Molecular typing showed that M. bovis 1595 has spoligotype SB0140 with mycobacterial interspersed repetitive units– variable number of tandem repeats typing of 4-2-5-3-2-7-5-5-4-3-4-3-4-3, representing the most common type of M. bovis in Korea. The complete genome sequence of strain 1595 was determined by single-molecule real-time technology, which showed a genome of 4351712 bp in size with a 65.64% G + C content and 4358 protein-coding genes. Comparative genomic analysis with the genomes of Mycobacterium tuberculosis complex strains revealed that all genomes are similar in size and G + C content. Phylogenetic analysis revealed all strains were within a 0.1% average nucleotide identity value, and MUMmer analysis illustrated that all genomes showed positive collinearity with strain 1595. A sequence comparison based on BLASTP analysis showed that M. bovis AF2122/97 was the strain with the greatest number of completely matched proteins to M. bovis 1595. This genome sequence analysis will serve as a valuable reference for improving understanding of the virulence and epidemiologic traits among M. bovis isolates in Korea.

Keywords: Korea, Mycobacterium bovis, cattle, genomics

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Figures and Tables

Fig. 1.

The entire genomic sequence of Mycobacterium bovis strain 1595. The scale is shown in megabases on the outer black circle. From the outside to the center: RNA features (ribosomal RNAs are shown in blue, and transfer RNAs are shown in red), genes on the forward strand, and genes on the reverse strand (colored according to the clusters of orthologous groups categories). The inner two circles show the GC ratio and GC skew. The GC ratio and GC skew shown in orange and red indicate positive values, respectively, and those shown in blue and green indicate negative values, respectively.

Fig. 2.

Genome tree based on the average nucleotide identity (ANI) values showing the relationships among Mycobacterium (M.) tuberculosis complex strains including M. bovis 1595. To convert the ANI value into a genetic distance, its complement to 1 was taken. From this pairwise distance matrix, an ANI tree was constructed using the unweighted pair group method and the arithmetic mean clustering method.

Fig. 3.

Nucleotide-based alignments with NUCmer. X-axis: Mycobacterium bovis strain 1595. Y-axis: (A) Mycobacterium bovis W-1171, (B) AF2122/97, (C) BCG Pasteur 1173P2, and (D) Mycobacterium tuberculosis H37Rv. Aligned segments are presented as dots or lines in the NUCmer alignment and were generated by the MUMmer plot script.

Table 1.

Clusters of orthologous groups (COGs) of the genome of Mycobacterium bovis strain 1595

COG	Description	Number of genes (n = 3,663)
J	Translation, ribosomal structure, and biogenesis	152 (4.15)
K	Transcription	232 (6.33)
L	Replication, recombination, and repair	214 (5.84)
D	Cell cycle control, cell division, chromosome partitioning	47 (1.28)
O	Posttranslational modification, protein turnover, chaperones	102 (2.78)
M	Cell wall/membrane/envelope biogenesis	118 (3.22)
N	Cell motility	20 (0.55)
P	Inorganic ion transport and metabolism	144 (3.93)
T	Signal transduction mechanisms	114 (3.11)
C	Energy production and conversion	214 (5.84)
G	Carbohydrate transport and metabolism	163 (4.45)
E	Amino acid transport and metabolism	204 (5.57)
F	Nucleotide transport and metabolism	72 (1.97)
H	Coenzyme transport and metabolism	123 (3.36)
I	Lipid transport and metabolism	219 (5.98)
Q	Secondary metabolites biosynthesis, transport, and catabolism	152 (4.15)
R	General function prediction only	403 (11.00)
S	Function unknown	970 (26.48)

Data are presented as number (%).

Table 2.

Genomic characteristics of strains used in this study

Characteristic	Mycobacterium (M.) bovis 1595	M. bovis W-1171	M. bovis AF2122/97	M. bovis BCG Pasteur1173P2	M. tuberculosis H37Rv
Genome size (bp)	4351712	4304865	4345492	4374522	4411532
%G + C	65.64	65.57	65.63	65.64	65.61
Status	Complete	Assembly	Complete	Complete	Complete
Contigs	1	50	1	1	1
CDSs	4,358	3,964	3,918	3,992	3,906
rRNA	3	3	3	3	3
tRNA	45	46	45	47	45

Contigs, contiguous; CDSs, coding sequences; rRNA, ribosomal RNA; tRNA, transfer RNA.

Table 3.

Similarities of open reading frames (ORFs) of various Mycobacterium (M.) tuberculosis complex strains compared to M. bovis 1595 (n = 4,358)

Match	M. bovis W-1171	M. bovis AF2122/97	M. bovis BCG Pasteur 1173P2	M. tuberculosis H37Rv
100%	3,515 (80.66)	3,657 (83.91)	3,396 (77.93)	3,237 (74.28)
99%	82 (1.88)	75 (1.72)	148 (3.40)	309 (7.09)
95%	73 (1.68)	45 (1.03)	96 (2.20)	89 (2.04)
90%	93 (2.13)	39 (0.89)	93 (2.13)	50 (1.15)
80%	24 (0.55)	37 (0.85)	30 (0.69)	49 (1.12)
70%	64 (1.47)	8 (0.18)	68 (1.56)	15 (0.34)
10%	45 (1.03)	17 (0.39)	40 (0.92)	38 (0.87)
Paralog	92 (2.11)	62 (1.42)	120 (2.75)	172 (3.95)
Missing	0 (0)	1 (0.02)	1 (0.02)	2 (0.05)
No match	370 (8.49)	417 (9.57)	366 (8.40)	397 (9.11)

Data present number (%) of ORFs.

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