刘朝阳, 朱永强, 徐樱妹, 赵悦烨, 朱调霞, 马雷钧, 陈哲文. 卡介苗生产用菌株全基因组测序[J]. 上海预防医学, 2023, 35(3): 213-218. DOI: 10.19428/j.cnki.sjpm.2023.22427
引用本文: 刘朝阳, 朱永强, 徐樱妹, 赵悦烨, 朱调霞, 马雷钧, 陈哲文. 卡介苗生产用菌株全基因组测序[J]. 上海预防医学, 2023, 35(3): 213-218. DOI: 10.19428/j.cnki.sjpm.2023.22427
shu
LIU Zhaoyang, ZHU Yongqiang, XU Yingmei, ZHAO Yueye, ZHU Tiaoxia, MA Leijun, CHEN Zhewen. Genome sequencing and analysis of BCG strain for vaccine production in China[J]. Shanghai Journal of Preventive Medicine, 2023, 35(3): 213-218. DOI: 10.19428/j.cnki.sjpm.2023.22427
Citation: LIU Zhaoyang, ZHU Yongqiang, XU Yingmei, ZHAO Yueye, ZHU Tiaoxia, MA Leijun, CHEN Zhewen. Genome sequencing and analysis of BCG strain for vaccine production in China[J]. Shanghai Journal of Preventive Medicine, 2023, 35(3): 213-218. DOI: 10.19428/j.cnki.sjpm.2023.22427
shu

卡介苗生产用菌株全基因组测序

Genome sequencing and analysis of BCG strain for vaccine production in China

    摘要
  • 摘要:
    目的 对我国生产用卡介苗上海D2PB302菌株（简称“卡介苗上海D2株”）全基因组进行测序及部分基因功能预测。
    方法 取卡介苗上海D2株（编号D2⁃JIA12⁃1）样品DNA，采用第三代测序平台PacBio RS Ⅱ进行全基因组测序，并结合二代测序数据得到最终的基因组序列。对基因序列分别进行rRNA预测和tRNA预测，对预测的基因进行基本的功能注释，并选取其中肺内表达结核分枝杆菌（MTB）在小鼠体内感染过程中高表达编码（IVE⁃TB）抗原基因序列、减毒结核分枝杆菌疫苗（MTBVAC）作为目的序列与结核分枝杆菌H37Rv序列（NC_000962.3）比对。
    结果 卡介苗上海D2株基因组序列长度为4 045 232 bp，GC含量为65.66%。Glimmer3.02软件共预测出4 259个基因，基因的平均长度为933 bp，其中1 783个基因是假定蛋白，其余2 476个基因具有明确的生物学功能，与毒力基因库比对后得到144个毒力基因，包含29个Ⅶ型分泌系统基因，10个N端具有保守的脯氨酸⁃谷氨酸（PE）和脯氨酸⁃脯氨酸⁃谷氨酸（PPE）序列的蛋白质家族基因。
    结论 明确了卡介苗上海D2株全基因序列的背景资料，并为后续开展主要抗原基因的遗传稳定性检测奠定了广泛的基础。

     

    Abstract:
    Objective To conduct the sequencing and preliminarily analysis of the whole genome of BCG Shanghai D2PB302 strain （hereinafter referred to as BCG Shanghai D2 strain）， which has been used exclusively for the vaccine production in China.
    Methods The DNA of of BCG Shanghai D2 strain （D2-JIA12-1） was extracted， and the whole genome was sequenced by Pacbio-RS Ⅱ. The sequence data was assembled by Smrtlink and polished with the illumina data. Genes， tRNA and rRNA were predicted based on the sequence data. The functional annotation of predicted genes was performed through BLASTP. The IVE-TB antigen gene and MTBVAC were selected as the target sequences to be compared with Mycobacterium tuberculosis H37Rv （NC_000962.3）.
    Results The sequence length of BCG Shanghai D2 strain was 4 045 232 bp， and the GC content was 65.66%. A total of 4 259 protein-encoding genes were predicted， with an average gene size of 933 bp. 2 476 genes had biological functions and others were hypothetical proteins.144 virulence genes were obtained by comparing with the VFDB. There were 29 type Ⅶ secretion system genes and 10 PE/PPE protein family genes.
    Conclusion The whole genome sequence of BCG Shanghai D2 strain is clarified. It lays a broad foundation for subsequent detection of the stability of major antigen genes.

     

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