Molecular characterization of two distinct monopartite begomoviruses infecting tomato in indiaReport as inadecuate




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Virology Journal

, 7:337

First Online: 23 November 2010Received: 03 August 2010Accepted: 23 November 2010

Abstract

BackgroundTomato leaf curl viruses, which are the members of the genus Begomovirus, have emerged as devastating pathogens worldwide causing huge economic losses and threatening production of crops like cassava, cotton, grain legumes and vegetables. Even though the ToLCV isolates from Northern India have been shown to possess bipartite genome designated as DNA A and DNA B, those from Australia, Taiwan and Southern India have a single genomic component DNA A. We describe here the genetic diversity of two isolates of monopartite Tomato leaf curl virus infecting tomato in two extreme regions North and South of Indian subcontinent.

ResultsThe rolling circle amplification RCA products obtained from symptomatic samples were digested, cloned and sequenced. The complete DNA sequence of two Tomato leaf curl virus isolates identified as ToLCV-CTM India, New Delhi, 2005 and ToLCVK3-K5 India, Kerala, 2008 are reported here. These isolates had the characteristic features of Begomovirus genome organization with six conserved open reading frames ORFs. The ToLCV-K3 and ToLCV-K5 isolates may be the strains of the same virus since they show sequence homology of 97% over their entire genome. This, according to the guidelines established by the ICTV Geminiviridae Study-Group is higher than threshold 92% for delineation of different viral variants and hence single, average value has been assigned for all their analyses presented here. The ToLCV-CTM and ToLCV-K3-K5 viruses were found to be monopartite, as neither DNA-B component nor betasatellite associated with begomovirus species, were detected. The complete nucleotide sequence of DNA-A genome of CTM exhibited highest sequence homology 88% to Croton yellow vein mosaic virus AJ507777, and of isolates K3-K5 88.5% to Tomato leaf curl Pakistan virus DQ116884. This is less than the threshold value for demarcation of species in the genus Begomovirus.

ConclusionK3-K5 and CTM are considered to be novel isolates of Tomato leaf curl virus. Sequence analyses and phylogenetic study indicate that these two ToLCV isolates might have evolved by recombination between viruses related to two or more viral ancestors. The existence of different ToLCV isolates having high genome diversity in India poses a threat to the tomato production in the Asian continent.

Electronic supplementary materialThe online version of this article doi:10.1186-1743-422X-7-337 contains supplementary material, which is available to authorized users.

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Author: Prerna Pandey - Subhra Mukhopadhya - Afsar R Naqvi - Sunil K Mukherjee - Gyan S Shekhawat - Nirupam R Choudhury

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