Molecular characterization of a distinct bipartite begomovirus species infecting tomato in India

Abstract

A distinct bipartite begomovirus was found associated with tomato plants showing yellowing, curling, and crumpling of the leaves, in a sub-temperate region in India. The complete DNA-A and DNA-B components were amplified through rolling circle amplification (RCA) using Phi-29 DNA polymerase and characterized. The DNA-A of the isolate was comprised of 2,756 nucleotides, encoding six open reading frames (ORFs) and DNA-B that of 2,725 nucleotides, encoding two ORFs. Genome organization of the isolate was typical of an old world bipartite begomovirus. Comparisons showed that DNA-A and its intergenic region (IR) have the highest sequence identity (86% and 84%, respectively) with the Tomato leaf curl New Delhi virus (ToLCNDV; DQ116885) and some other begomoviruses (>84%) reported from cucurbits and tomato. This data suggested that the isolate is a distinct begomovirus species for which a name Tomato leaf curl Palampur virus (ToLCPMV) is proposed. DNA-B showed the maximum sequence identity (73%) with Tomato leaf curl New Delhi virus-India-[Pakistan:Dargai:T5/6:2001] (AY150305). The common region (CR) of DNA-A and DNA-B showed 94% sequence similarity with each other. In the present study, phylogenetic relationship of this new species was also established with different begomoviruses reported from tomato and other begomoviruses showing highest homologies with complete DNA-A and DNA-B sequences. ToLCPMV is being reported from a sub-temperate region in India which was previously unaffected by begomoviruses and its whitefly vector.

Velvet bean severe mosaic virus: a distinct begomovirus species causing severe mosaic in Mucuna pruriens (L.) DC

“…Characterization of novel DNA viruses and construction of the infectious clones has become easier with the use of /-29 DNA polymerase, which selectively amplifies the circular DNA by rolling circle mechanism [12][13][14].…”

Tomato yellow leaf curl Thailand virus-[Y72] from Yunnan is a monopartite begomovirus associated with DNAβ

“…However, all the seven TYLCTHV isolates collected from tomatoes in Yunnan Province of China were associated with DNAb molecules, rather than DNA-B components [5]. Most of the tomato-infecting [6,9,[16][17][18]. So, it is interesting to elucidate the monopartite or bipartite nature of TYLCTHV.…”

Detection and characterization of Ageratum enation virus and a nanovirus-like satellite DNA1 from zinnia causing leaf curl symptoms in India

“…Begomoviruses cause huge economic losses to food and fiber crops worldwide, mainly in tropical and subtropical parts of the world (Varma and Malathi 2003). As a result of global warming, greenhouse cultivation, the appearance and increase in the population of whitefly biotype B and its intrusion into new areas, begomovirus diseases are emerging as serious problems in more temperate areas in India (Kumar et al 2008). The majority of the begomoviruses are bipartite, but many monopartite begomoviruses have been characterized, usually associated with DNA satellites that are required for symptom induction .…”

“…All four samples were positive for AEV, and the sequences had very high ([99%) sequence similarity with each other. Hence, only one sample was taken for complete genome characterization by rolling circle amplification (RCA) using a TempliPhi DNA Amplification Kit (GE Healthcare, Piscataway, NJ, USA) and a protocol described previously (Kumar et al 2008). In RCA, /-29 DNA polymerase selectively amplifies only circular DNA, and the technique has revolutionized genomic studies of geminiviruses (Haible et al 2006).…”