Molecular evidence of Apple stem grooving virus infecting Ficus palmata

Abstract

The present study identified Ficus palmata as a new natural host of Apple stem grooving virus. Ficus palmata, growing in the campus of CSIR-IHBT, was found to exhibit virus-like symptoms which include necrotic and chlorotic spots, chlorosis, leaf deformation and marginal chlorosis. Surveys were conducted in three different areas of district Kangra; leaf samples from symptomatic and asymptomatic plants were collected and subjected to DAS-ELISA, NASH and RT-PCR. Combined results of the three detection techniques revealed the presence of ASGV in 15/30 tested samples, thereby confirming the presence of ASGV in 50% of the samples. Out of the 15 positive samples, 5 randomly selected samples were confirmed at the molecular level through sequencing of the partial replicase gene of ASGV and complete CP gene sequences were used for characterization and phylogenetic analysis. Further, all the five positive samples were also analyzed for any probable mixed infection of major apple viruses, viz., Apple stem grooving virus (ASGV), Apple chlorotic leafspot virus (ACLSV), Apple stem pitting virus (ASPV) and Apple mosaic virus (ApMV) by multiplex RT-PCR. The results revealed that the samples were positive only for ASGV. The phylogenetic analysis based upon the CP gene revealed that the five characterized isolates (Fi-15, Fi-16, Fi-19, Fi-20 and Fi-29) were grouped into two separate clusters and shared 88.5–100% (nt) and 95.3–100% (aa) sequence identity among themselves. Out of the five, four isolates (Fi-15, Fi-19, Fi-20 and Fi-29) were 100% identical to each other, while they shared 88.5 and 95.3% sequence identity with the fifth isolate (Fi-16) at nucleotide (nt) and amino acid (aa) levels, respectively. Further among the five isolates, the variant Fi-16 isolate was used for mechanical inoculation on herbaceous hosts. Mechanical inoculation studies of the variant Fi-16 isolate revealed that this isolate could be successfully transmitted mechanically to Chenopodium amaranticolor, Cucumis sativus, Chenopodium quinoa, Phaseolus vulgaris, Nicotiana benthamiana and Nicotiana glutinosa. To the best of our knowledge, this is the first report of F. palmata as a new natural host of ASGV.