ABSTRACT

Garlic virus A (GarV-A) severely damages and reduces the yield of economically important garlic crop worldwide. Here, we present the first comprehensive view of GarV-A infecting Yamuna Safed-3 (G282) of garlic (Allium sativumL.) variety from India at the complete genome sequence level. RNA-seq was performed on an Illumina HiSeq 2000 platform to obtain the full length GarV-A genome and analysed by different software and reverse transcription-polymerase chain reaction (RT-PCR) confirmed the presence of the GarV-A. The virus complete genome consists of 8,793 nucleotides (nt), excluding the poly (A) tail at the 3ʹ terminus, with 5ʹ and 3ʹ untranslated regions (UTRs) of 193 and 123 nt, respectively. Genome analysis of GarV-A Indian isolate shared higher nucleic acid and amino acid sequence identity to Chinese isolates than to Australian and Spanish isolates. Further RDP analysis showed that the Indian GarV-A (MT731489) isolate was found to be recombinant with most part of the RNA segment is derived from China GarV-E isolate (MN059326) as the minor parent and the Russia ShV-X (JX310755) isolate as the major parent. More research is needed to determine the outspread of this particular recombinant virus. This is the first report of the complete genome sequence and evidence of homologous recombination in of GarV-A from India.