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

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.

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.