Biological and Molecular Characterization of Two Distinct Tomato Strains of Cucumber mosaic virus Based on Complete RNA-3 Genome and Subgroup Specific Diagnosis

Abstract

Cucumber mosaic virus (CMV) is one of the most important viral pathogen infecting several plant species in India. Five isolates of CMV obtained from cucumber, muskmelon, tobacco and tomato from distinct geographical locations in India were analysed based on host-reactions and genome sequence. The majority of the isolates were very similar and only two isolates, Tfr-In and Tss-In showed distinct symptoms in tomato and high sequence diversity (77.8%) in coat protein (CP) gene. Tfr-In was isolated from tomato fruit showing grey patches in Aurangabad and Tss-In from tomato plant showing shoe-string symptoms in New Delhi. The RNA-3 genomes of Tfr-In (2,214 nt; JF279606), shared only 70.3% nucleotide sequence identity with Tss-In (2,178 nt; JF279605. The complete RNA-3 genome of Tss-In and Tfr-In were compared with that of 65 CMV isolates reported from various plants of the world, which formed four distinct subclades-IA, -IB, -IC and -II. The Tfr-In isolate clustered with the CMV subgroup-IB and Tss-In with the subgroup-II. The comparison of the RNA-3 sequence of both the isolates revealed maximum heterogeneity in the intergenic region (IR). Reverse transcriptase polymerase chain reaction (RT-PCR) based detection of CMV subgroup-I and -II was developed designing primers from flanking IR region. The specificity of the RT-PCR detection was confirmed using Tfr-In and Tss-In representing subgroup-I and -II and validated with field samples of tomato, cucurbits and chilli. This is the first report of complete RNA-3 of subgroup-IB CMV causing grey patches in tomato fruit and subgroup-II CMV causing shoe-string symptoms in tomato in India. The present and previous studies together showed that tomato in India was affected by multiple strains of CMV.

Biological and Molecular Characterization of Cucumber mosaic virus Isolate Causing Shoestring Disease of Tomato in India which has Closer Affinity to European or East Asian Isolates of CMV

“…RNA3 genome based characterization of three distinct tomato strains of CMV have been reported recently from India [8,26]. We further report, the biological and molecular characterization of CMV isolate retrieved from tomato which has closer affinity to European or East Asian CMV isolates than to other isolates previously characterized in India.…”

Biological and Molecular Characterization of Cucumber mosaic virus Subgroup II Isolate Causing Severe Mosaic in Cucumber

“…Mainly, subgroup I isolates has been reported and there are few reports of subgroup II isolates [1,15,47,53]. The isolate under study showed up to 99 and 76 % similarity to the subgroup II and I isolates, respectively.…”

“…From India also there was report of mosaic symptoms on tomato by subgroup II strain [47] and now in a recent observation it was found that shoestring symptoms were not restricted to subgroup I. A subgroup II isolate Tss-In developed shoestring symptoms on tomato [15]. Cryoelectron microscopy of purified virus showed the presence of *28 nm isometric particle size, its SDS-PAGE and western blotting showed CP of *26 kDa and its dimeric form at *52 kDa.…”

“…Broad host range of CMV from subgroup I and II have been identified in India, which includes: Chrysanthemum [45]; Ocimum sanctum and Zinnia elegans [34]; Amaranthus tricolor, Datura innoxia and Hyoscyamus muticus [44]; Gerbera [53]; Vanilla [28]; Pelargonium [52]; Piper longum and Piper betel [19]; Rouvolfia serpentine [35]; Jatropha curcas [36]; Catharanthus roseus [40]; Daucas carrota [1]; Banana [24,29]; Lycopersicum esculentum [15,25,47]; Gladiolus [13]. Although many CMV strains were isolated from India, but incomplete information is available at the genome level about these isolates.…”

Multiple functions of capsid proteins in (+) stranded RNA viruses during plant–virus interactions

“…The degree of CPRG downregulation followed the severity of chlorosis, indicating that CP mutations governed (directly or indirectly) the repression of CPRG mRNAs. The link of CP with symptoms seems to be strengthened with CMV isolates that were obtained from cucumber, muskmelon, tobacco, and tomato from distinct geographical locations in India (Swapna Geetanjali et al, 2011). The majority of the isolates were very similar but two isolates, Tfr-In and Tss-In showed distinct symptoms in tomato alongside the high sequence diversity in the CP gene.…”