菠萝杆状DNA病毒的全基因组序列测定及分析

Sequencing and Analysis of the Complete Genomic Sequence of Pineapple bacilliform comosus virus

【目的】证明中国湛江地区菠萝上是否存在菠萝杆状DNA病毒(Pineapple bacilliform comosus virus,PBCoV),并获得PBCoV的基因组全序列,分析该病毒与其它Badnavirus病毒分离物间的分子差异。【方法】设计特异引物,通过反向PCR及分段克隆两种方法扩增PBCoV,克隆后测序获得PBCoV基因组全序列,利用不同生物学软件进行序列分析。【结果】PBCoV基因组为环状结构,全长7543bp;含有3个典型的ORFs,推测其编码蛋白的分子量分别为20.4、14.0和217.6kD。其基因组与GenBank登录的PBCoV ORF3部分核苷酸序列同源性87%-97%,其ORF3编码的氨基酸序列与已报道的Badnavirus病毒ORF3氨基酸序列间一致率小于50.8%。Southern blot分析显示该病毒基因组能整合到植物基因组中。【结论】在中国湛江地区菠萝上存在PBCoV,该病毒属于Badnavirus属病毒,与香蕉线条病毒(Banana streak virus)Mys分离物(BSV-Mys)亲缘关系最近。这是PBCoV基因组全序列的首次报道。

Objective Pineapple bacilliform comosus virus （PBCoV） was identified on pineapple in Zhanjiang district, Guangdong province, China, and the complete genomic sequence of PBCoV was analyzed and compared in the molecular variation among Badnaviruses. Method The specific primers of PBCoV were designed, and the viral partial and whole genomic sequences were, respectively, amplified with regular or inverse PCRs and analyzed by proper bioinformatics softwares. Result The complete circular genomic nucleotide sequence of PBCoV comprised 7 543 bp, which contained 3 ORFs on the plus-strand that potentially encoded proteins of 20.4, 14.0 and 217.6 kD, respectively. The nucleotide sequences of PBCoV shared 87%-97% identities with the partial sequences of PBCoV from Australia in GenBank. The amino acid sequence encoded by the viral ORF3 shared less than 50.8% identities with that of any known Badnaviruses. Evidence that the PBCoV sequence is integrated in the pineapple genome was presented and discussed. Conclusion The results indicated that PBCoV exists on pineapple in Zhangjiang district, Guangdong province, China. The virus belongs to Badnavirus, which shares the most identities in nucleotide level with Banana streak virus-Mys isolate. This is first to report the complete genomic sequence and structure of PBCoV.