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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 Kim1, 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 Kim1, *

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

Copyright © 2017 The Korean Society of Veterinary Science

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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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.
jvs-18-333f1.tif
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.
jvs-18-333f2.tif
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.
jvs-18-333f3.tif
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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