Molecular Characterization and Diagnosis of Virus Infecting Garlic (Allium Sativum)

Abstract

Garlic (Allium sativum L.) widely used as a spice and medicine all around the globe due to its high nutritive and medicinal properties. Even though fungal and bacterial diseases are the most devastating, viral diseases are also important to garlic plants considering the vegetative propagating nature of garlic and transmission of viruses leading to decrease in yields and deterioration of quality. Garlic viruses often occur in mixed infections under field conditions. In the present study we report the first comprehensive view of multiple virus infecting garlic- Yamuna Safed-3 (G282) from India at near complete genome level. RNA-seq was performed on an Illumina HiSeq 2000 platform, total of 34,873,376 and 31,497,569 paired end sequence reads were generated and after de novo assembly of garlic transcriptome which generated 131305 and 108668 contigs in garlic clove and leaf transcriptome, respectively. The blast analysis revealed that, in addition to near to complete genome sequence of Allexivirus- Garlic Virus A (GarV-A) (MT731489, MT731490),Garlic Virus D (GarV-D) (MK518067),Garlic Virus X (GarV-X (MT731498, MT731499), Carlavirus- Garlic common latent virus (GCLV) (MT731496), Poty viruses-OYDV (MT731493, MT731494, MT731493) and LYSV (MT731491, MT731492) were obtained and submitted to GenBank.The PCR based validation was performed for Garlic Virus A, Garlic Virus D and Garlic Virus X from samples collected from the fields. We examined the sequence variability, distribution of simple sequence repeats (SSRs), entropy of different genes, and recombination breakpoints of different virus(s) geographical isolates of Allexivirus, Carlavirus and Potyvirus discussed in the study. Therefore, knowledge of the complete genome, recombination events, microsatellite distribution microsatellite (SSR) pattern distribution described in the study may have several important functions related to evolutionary dynamics, gene expression modulation and virus genome organization. The evidence concerning the incidence of garlic viruses is significant for virus indexing for virus-free propagative material as well as breeding for virus resistance of the new garlic cultivars to the investigated viruses.