苹果茎痘病毒在山楂中的首次鉴定与序列分析

山楂是我国重要的果树,但山楂病毒的相关研究较少.本研究通过高通量测序及生物信息学分析首次在山楂样品中发现苹果茎痘病毒(apple stem pitting virus,ASPV).利用RT-PCR和cDNA末端快速扩增技术对ASPV山楂分离物全长序列进行扩增,结果表明,ASPV山楂分离物基因组全长由9 290个核苷酸组...

Identification and sequence analysis of apple stem pitting virus from hawthorn tree

Hawthorn is a kind of important fruit crop in China, while the associated researches on hawthorn viruses are very limited. We performed high-throughput sequencing and bioinformatics analysis on the hawthorn leaves and identified apple stem pitting virus (ASPV) in hawthorn samples for the first time. The whole genome of ASPV hawthorn isolate was obtained by RT-PCR. Bioinformatics analysis showed that the complete genome consists of 9 290 nucleotides (nt), including five open reading frames (ORFs). The ORF1 of the ASPV hawthorn isolate which encodes replication-associated protein RNA dependent RNA polymerase (RdRp) shared 72.8%-80.9% and 81.7%-92.8% with those isolates from apples and pears at nt and amino acid levels; ORFs 2-4 contains a triple gene block (TGB 1-3), and the amino acid sequence shows the highest similarity to ASPV Indian Apple N isolate (LM999967) of 92.9%-98.2%; ORF5 encodes the coat protein (CP) and has a relatively low similarity compared with CPs of apple and pear isolates (64.8%-88.4% and 69.8%-92.2%, respectively), which is higher than the current demarcation of new virus species. The whole nucleotide sequence of ASPV hawthorn isolate was aligned with other isolates and phylogenetic tree was constructed, which showed that ASPV hawthorn isolate was most closely related to BR-Brae2 isolate from apple in Brazil despite a relatively low nucleo-tide sequence identity (81.5%), indicating that the isolate had great variability. Above all, this study preliminarily confirmed that hawthorn is an important natural host of ASPV, and we obtained the full-length genome sequence of ASPV isolate for the first time, which provided references for diagnosis, prevention and control strategy formulation of hawthorn viruses.