Molecular characterization of a naturally occurring intraspecific recombinant begomovirus with close relatives widespread in southern Arabia.

Mohammed A Al-Saleh,Ali M Idris,Ibrahim M Al-Shahwan,Judith K Brown

doi:10.1186/1743-422x-11-103

Abstract

BackgroundTomato leaf curl Sudan virus (ToLCSDV) is a single-stranded DNA begomovirus of tomato that causes downward leaf curl, yellowing, and stunting. Leaf curl disease results in significant yield reduction in tomato crops in the Nile Basin. ToLCSDV symptoms resemble those caused by Tomato yellow leaf curl virus, a distinct and widespread begomovirus originating in the Middle East. In this study, tomato samples exhibiting leaf curl symptoms were collected from Gezira, Sudan. The associated viral genome was molecularly characterized, analyzed phylogenetically, and an infectious clone for one isolate was constructed.FindingsThe complete genomes for five newly discovered variants of ToLCSDV, ranging in size from 2765 to 2767-bp, were cloned and sequenced, and subjected to pairwise and phylogenetic analyses. Pairwise analysis indicated that the five Gezira isolates shared 97-100% nucleotide identity with each other. Further, these variants of ToLCSDV shared their highest nucleotide identity at 96-98%, 91-95%, 91-92%, and 91-92% with the Shambat, Gezira, Oman and Yemen strains of ToLCSDV, respectively. Based on the high maximum nucleotide identities shared between these ToLCSDV variants from Gezira and other previously recognized members of this taxonomic group, they are considered isolates of the Shambat strain of ToLCSDV. Analysis of the complete genome sequence for these new variants revealed that they were naturally occurring recombinants between two previously reported strains of ToLCSDV. Finally, a dimeric clone constructed from one representative ToLCSV genome from Gezira was shown to be infectious following inoculation to tomato and N. benthamiana plants.ConclusionFive new, naturally occurring recombinant begomovirus variants (>96% shared nt identity) were identified in tomato plants from Gezira in Sudan, and shown to be isolates of the Shambat strain of ToLCSDV. The cloned viral genome was infectious in N. benthamiana and tomato plants, and symptoms in tomato closely resembled those observed in field infected tomato plants, indicating the virus is the causal agent of the leaf curl disease. The symptoms that developed in tomato seedlings closely resembled those observed in field infected tomato plants, indicating that ToLCSDV is the causal agent of the leaf curl disease in Gezira.

Highlights

Tomato leaf curl Sudan virus (ToLCSDV) is a single-stranded DNA begomovirus of tomato that causes downward leaf curl, yellowing, and stunting
Two species have been reported from the Nile Basin, Tomato leaf curl Sudan virus (ToLCSDV) and Tomato yellow leaf curl virus (TYLCV) [2,3], while three species have been recognized in the southern region of Arabia, Tomato leaf curl Oman virus (ToLCOMV), ToLCSDV and TYLCV [1,4]
In a recent example reported from three locations in South America, the DNA-B component was shown to be dispensable for systemic infection [13,14], whereas, in another study involving infectious DNA-A component, no cognate DNA-B was detected [15]

Summary

Introduction

Tomato leaf curl Sudan virus (ToLCSDV) is a single-stranded DNA begomovirus of tomato that causes downward leaf curl, yellowing, and stunting. Two species have been reported from the Nile Basin, Tomato leaf curl Sudan virus (ToLCSDV) and Tomato yellow leaf curl virus (TYLCV) [2,3], while three species have been recognized in the southern region of Arabia, Tomato leaf curl Oman virus (ToLCOMV), ToLCSDV and TYLCV [1,4] This collective group of monopartite begomoviruses causes extensive damage to tomato (Solanum lycopersicum L.) crops in the arid and semi-arid southern part of the Arabian Peninsula and the Nile Basin [2,5]. Begomoviruses are characterized by having a single-stranded circular DNA genome encapsidated in twinned icosahedral particles, and recently, have emerged to cause debilitating diseases to many species of dicotyledonous plants of agricultural importance [6] They are widespread in uncultivated, endemic and naturalized plant species found in the tropics and subtropics worldwide [7,8]. In a recent example reported from three locations in South America, the DNA-B component was shown to be dispensable for systemic infection [13,14], whereas, in another study involving infectious DNA-A component, no cognate DNA-B was detected [15]

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Conclusion