Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain M1601

GENOME ANNOUNCEMENT

Mycoplasma capricolum subsp. capripneumoniae is the causative agent of contagious caprine pleuropneumonia (CCPP). CCPP is one of the important bacterial epizootics that cause considerable economic losses of goats in Africa and Asia. It is included in the list of notifiable diseases of the World Organization for Animal Health (7). We have sequenced the complete genome of M. capricolum subsp. capripneumoniae to facilitate related studies in the future.

M. capricolum subsp. capripneumoniae strain M1601 is an isolate from a goat with CCPP in China (4). Whole-genome sequencing was performed on the Illumina GA using one flow cell lane with 36-cycle paired-end chemistry. We produced 73,559,926 sequences of 76-bp shotgun reads. The total of 1,018,102 sequenced bases was used for assembly, representing a sequencing depth of 5,491. The de novo assembly was done using ABySS (6) and produced 12 contigs of at least 200 bp. These 12 contigs were ordered and oriented by mapping to Mycoplasma capricolum subsp. capricolum (NC_007633.1) using MUMmer, resulting in a single contig of 1,016 kbp with one small gap of about 1 kb in the assembly due to a simple repetitive sequence. Thus, the genome of M1601 consists of a single chromosome comprising 1,018,102 bp with a relatively low GC content of 23.29%.

The complete sequence was analyzed by Glimmer3.0 (1) for gene predication; tRNAscan (5) and Aragorn (3) for the tRNA and tmRNA genes; and RNAmmer (2) for the rRNA genes. We found 961 open reading frames (ORFs) in the genome with an average gene length of 824 bp. There are two rRNA operons, 30 tRNA genes, and 1 tmRNA gene. The coding density of the genome is 77.85%. The functions of the predicted protein-coding genes were annotated by blasting based on the Swiss-Prot and TrEMBL (release 2010-04), COG (version 2.0), KEGG (release 48.2), and NCBI-NR (release 2010-8-7) databases. A total of 875 (91.05%) ORFs were annotated. We classified 531 genes (55.25%) into COG families comprising 18 functional categories; 241 (25.08%) of them are involved in transport and metabolism. Among these genes, we found some recognizable genes likely to be associated with virulence. The genome contains a gene cluster involved in the synthesis of the capsule, comprising genes encoding putative glycosyltransferases and UTP-glucose-1-phosphate uridylyltransferase. Both the glpF, glpK, and glpD gene cluster and the gtsA, gtsB, and gtsC gene cluster, involved in glycerol import and production of H₂O₂, were identified. The lppB gene, encoding a lipoprotein precursor, is located immediately downstream of the second gene cluster. Hemolysin A (hlyA), which has been found in other mycoplasmas (8), is present, but its contribution to the pathogenicity of this mycoplasma is unclear. There are 8 genes coding for putative variable surface proteins thought to be involved in antigenic variation in this mycoplasma strain.

This is the first complete genome sequence of M. capricolum subsp. capripneumoniae.