菊花R病毒杭白菊分离株全基因组序列测定与分析

Identification and Analysis of Complete Genomic Sequence of Chrysanthemum Virus R Isolated from Chrysanthemum morifolium

杭白菊作为著名的中药"浙八味"之一,种植规模和产区不断扩大,但其病毒病的发生也日益严重,对其产量和品质造成严重影响。本研究利用双链RNA(double-stranded RNA,dsRNA)和非序列依赖PCR扩增(sequence-independent amplification,SIA)等方法,对感病杭白菊病原物进行鉴定,为杭白菊病毒病原的检测构建一套快速和简便的方法。结果表明,感病杭白菊被菊花R病毒(Chrysanthemum virus R,CVR)侵染,将其命名为CVR-TX。通过对其全基因组进行序列扩增与分析,获得其全长基因组为8872 bp,编码6个ORF,具有Carlavirus属病毒的典型特征。基于全基因组核酸序列以及复制酶、外壳蛋白氨基酸的序列比对发现,CVR-TX与CVR-BJ同源性最高,分别为85.5%、96.0%和96.3%;与Carlavirus属其他病毒同源性分别在48.2%~54.4%、46.9%~55.3%和36.8%~59.5%,因此CVR被确定为一种新的Carlavirus属病毒。系统进化分析表明,基于全长基因组、复制酶(replicase)基因和外壳蛋白(coat protein,CP)基因与CVR-BJ聚为一簇,亲缘性最近。本研究获得了CVR-TX的全长基因组,丰富了CVR的基因组信息,通过生物信息学分析明确其种属关系和区域变化情况,从而为建立CVR可靠灵敏的分子检测手段和有效的防控措施提供理论基础。

As one of the famous Chinese medicinal drugs"Eight flavors of Zhejiang",the planting scale and producing areas of Chrysanthemum of Hangzhou have been expanding,but the occurrence of viral disease has become more and more serious,which has seriously affected its yield and quality.In this study,double-stranded RNA(dsRNA)and sequence-independent amplification(SIA)were used to identify the pathogens of Chrysanthemum,and a rapid and simple method was constructed for the detection of chrysanthemum viral disease.The results indicated that the Chrysanthemum was infected by Chrysanthemum virus R(CVR)and it was named CVR-TX by us.Through sequence amplification and analysis of the whole genome,it was found that the full-length genome was 8872 bp,with typical characteristics of the genus Carlavirus and encoding 6 ORFs.Based on the whole genome nucleic acid sequence and sequence alignment of replicase and CP amino acids,CVR-TX and CVR-BJ have the highest homology,which are 85.5%,96.0%and 96.3%,respectively;the homology with other Carlaviruses was 48.2%-54.4%,46.9%-55.3%and 36.8%-59.5%,respectively;so CVR was identified as a new Carlavirus.The phylogenetic trees based on complete genome,Replicase and Coat protein(CP)sequences showed CVR-TX were clustered with CVR-BJ,with the closest affinity.The full-length genome of CVR-TX was obtained in this study,which enriched the genomic information of CVR,and clarified its species relationship and regional variation through bioinformatics analysis,thus providing a theoretical basis for establishing reliable and sensitive molecular detection method and effective prevention and control measures for CVR.