Genome-Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships

Abstract

Mycoplasma bovirhinis is a significant etiology in bovine pneumonia and mastitis, but our knowledge about the genetic and pathogenic mechanisms of M. bovirhinis is very limited. In this study, we sequenced the complete genome of M. bovirhinis strain GS01 isolated from the nasal swab of pneumonic calves in Gansu, China, and we found that its genome forms a 847,985 bp single circular chromosome with a GC content of 27.57% and with 707 protein-coding genes. The putative virulence determinants of M. bovirhinis were then analyzed. Results showed that three genomic islands and 16 putative virulence genes, including one adhesion gene enolase, seven surface lipoproteins, proteins involved in glycerol metabolism, and cation transporters, might be potential virulence factors. Glycerol and pyruvate metabolic pathways were defective. Comparative analysis revealed remarkable genome variations between GS01 and a recently reported HAZ141_2 strain, and extremely low homology with others mycoplasma species. Phylogenetic analysis demonstrated that M. bovirhinis was most genetically close to M. canis, distant from other bovine Mycoplasma species. Genomic dissection may provide useful information on the pathogenic mechanisms and genetics of M. bovirhinis.

Keywords: Genome Report; Mycoplasma bovirhinis; comparative analysis; genome; phylogenetic analysis; virulence gene.

Figure 1

Chromosome atlas of Mycoplasma bovirhinis strain GS01. dnaA at position 1. From outer to inner circles, the first circle represents the genome position coordinates; the second circle shows the locations of predicted coding genes on plus and minus strands; the third, fourth, and fifth circles show the results of color-coded by COG categories, KEGG, and GO annotation (see the description at the bottom-right corner), respectively; the sixth circle represents the ncRNA in GS01 genome; the seventh circle represents the mean centered G+C content whose baseline is average GC, and outward and inward projections express higher and lower values than the average, respectively; and the eighth circle illustrates the GC (G+C) skew plot: above and below zero are highlighted in green and purple, respectively.

Figure 2

Collinearity analysis of the complete genome between M. bovirhinis strain GS01 and HAZ141_2. (a): Two genomes on parallel collinearity. The upper and lower shafts represent the sequenced and reference genomes, respectively. The orange box in the axes indicates the genomic forward strand, and the blue one corresponds to the reverse chain. The filled color in the box denotes alignment similarity, and the complete filling suggests 100% similarity. The color of the link graph between the upper and lower axes represents alignment type: pink, purple, yellow, and green denote collinear, translocation, inversion, and translocation+inversion, respectively. (b): Two-dimensional comparison between two genomes. The vertical and horizontal axes represent GS01 genome and reference HAZ141_2 genome, respectively. The blue line shows the reverse chain, and the red line corresponds to forward alignment. The pink and green modules indicate collinear and translocation+inversion between them, respectively.

Figure 3

Phylogenetic trees of 14 single-copy core genes of 19 selected Mycoplasma strains. (a): Phylogenetic tree was constructed using TreeBeST with the maximum likelihood model. Bootstrap replicates were 1000, and the number of bootstraps for each node is shown. The tree is displayed to scale, with branch lengths measured in the number of substitutions per site. M. bovirhinis strain GS01 is indicated by a black dot. (b): Phylogenetic tree was constructed using MrBayes with bayesian inference method. The numbers upon each node indicate bayesian posterior probabilities. The tree is displayed to scale, with branch lengths measured in the number of substitutions per site. M. bovirhinis strain GS01 is indicated by a black dot.