甘薯病毒G CH株系和CH2株系中国分离物基因组全序列克隆及结构特征分析

Complete nucleotide sequence and characterization analysis of the sweet potato virus G CH and CH2 strains isolated from China

为明确甘薯病毒G(sweet potato virus G,SPVG)CH株系中国分离物SPVG-CH-Ch1和CH2株系中国分离物SPVG-CH2-Ch1的基因组结构特征及遗传变异情况,利用RT-PCR和RACE方法克隆获得分离物SPVG-CH-Ch1和SPVG-CH2-Ch1的基因组全序列,应用DNAMAN软件对基因组全序列及不同编码区序列进行分子变异分析,并基于多聚蛋白基因序列利用MEGA 7软件进行系统进化分析。结果表明,分离物SPVG-CH-Ch1和SPVG-CH2-Ch1的基因组分别包含10 813个和10 834个核苷酸,均包含1个开放阅读框,由10 467个核苷酸组成,编码含有3 488个氨基酸残基的多聚蛋白。分离物SPVG-CH-Ch1与SPVG-CH2-Ch1之间的基因组全序列核苷酸一致性为78.6%,二者与GenBank中登录的其它SPVG分离物基因组全序列核苷酸一致性分别为78.6%~99.1%和77.9%~98.6%,其中SPVG-CH-Ch1与IS103分离物(KM014815)的核苷酸一致性最高,为99.1%,与WT325分离物(KF790759)的核苷酸一致性最低,为78.6%;SPVG-CH2-Ch1与WT325分离物的核苷酸一致性最高,为98.6%,与66Al分离(KX279878)的核苷酸一致性最低,为77.9%。系统进化树显示,SPVG-CH-Ch1与CH株系的7个分离物形成1个分支,SPVG-CH2-Ch1与CH2株系的WT325分离物形成1个分支。表明SPVG的CH株系和CH2株系之间的变异较大,株系内较保守。

In order to elucidate the complete genomic organization and molecular variability of the sweet potato virus G(SPVG) CH and CH2 strains isolated from China, which named SPVG-CH-Ch1 and SPVG-CH2-Ch1, the complete genomic sequences of them were amplified by RT-PCR and RACE,genetic variation analysis of complete genomic sequences and individual protein sequences were performed using DNAMAN, and neighbor-joining phylogenetic tree of them with other isolates was generated using MEGA 7.0 software. The results showed that the complete genomic sequence of the two isolates were 10 813 nucleotides(nt) and 10 834 nt in length, respectively. The genomic organizations of the two isolates contained one open reading frame of 10 467 nt encoding a polyprotein of 3 488 amino acids. The SPVG-CH-Ch1 isolate exhibited nt sequence identity of 78.6% with SPVG-CH2-Ch1 isolate.Pairwise comparisons showed that SPVG-CH-Ch1 and other SPVG isolates deposited in GenBank database shared 78.6%-99.1% nt sequence identity at the complete genomic sequence level. It was most closely related to the isolate IS103(KM014815) with 99.1% nt identity and showed the lowest nt identity with isolate WT325(KF790759) by 78.6%. SPVG-CH2-Ch1 and the other SPVG isolates shared77.9%-98.6% nt sequence identity at the complete genomic sequence level. It had the highest nt identity with isolate WT325(KF790759) by 98.6%, and the lowest nt identity with isolate 66 Al(KX279878)by 77.9%. Phylogenetic tree analysis based on the polyprotein gene placed SPVG-CH-Ch1 isolate in CH strain and SPVG-CH2-Ch1 in CH2 strain containing WT325. The results indicated that SPVG had great genetic variability between CH and CH2 strains, but high degree of conservation in strains.