JOURNAL OF BACTERIOLOGY, Nov. 2011, p. 6098–6099 0021-9193/11/$12.00 doi:10.1128/JB.05980-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Vol. 193, No. 21
Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain M1601 Yuefeng Chu,1 Pengchen Gao,1 Ping Zhao,1 Ying He,1 Nancy Liao,3 Shaun Jackman,3 Yongjun Zhao,3 Inanc Birol,3 Xiaobo Duan,1,2* and Zhongxin Lu1* State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Epizootic Diseases of Grazing Animals of Ministry of Agriculture, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China1; Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada2; and Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada3 Received 9 August 2011/Accepted 17 August 2011
Mycoplasma capricolum subsp. capripneumoniae is the causative agent of contagious caprine pleuropneumonia, a devastating disease of goats listed by the World Organization for Animal Health. Here we report the first complete genome sequence of this organism (strain M1601, a clinically isolated strain from China).
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. Nucleotide sequence accession numbers. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/ GenBank under accession no. AENG00000000. The version described in this paper is the first version and is available under accession no. AENG01000000.
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
This work was supported by the Technology R&D program of Gansu Province (1011NKCA054), the Natural Science Foundation of Gansu Province (1107RJZA107), Gansu Province Agricultural Biotechnology Research and Application Development Projects (GNSW2010-09), the National Scientific-Basic Special Fund (2008FY210200), and the China Agriculture Research System (CARS-39).
* Corresponding author. Mailing address for Zhongxin Lu: Lanzhou Veterinary Research Institute of CAAS, Xujiaping 1, Yanchangbu, Lanzhou 730046, Gansu, China. Phone: 86-931-8342676. Fax: 86-9318340977. E-mail:
[email protected]. Mailing address for Xiaobo Duan: Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, 2410 Lee Avenue, Victoria, British Columbia V8R 6V5, Canada. Phone: (250) 519-5715. Fax: (250) 5192420. E-mail:
[email protected].
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