Sequence characterization of cotton leaf curl virus from Rajasthan: phylogenetic relationship with other members of geminiviruses and detection of recombination

Abstract

Diseased cotton plants showing typical leaf curl symptoms were collected from experimental plot of Agriculture Research Station-Sriganganagar, Rajasthan. Complete DNA-A component from samples taken from two areas were amplified through rolling circle amplification (RCA) using templiphi kit (GE Healthcare) and characterized. DNA-A of one isolate consists of 2751 nucleotides and second isolate of 2759 nucleotide. Both sequences comprised six ORF's. Genome organization of DNA-A of one isolate shows high sequence similarity with other characterized local begomovirus isolates of Rajasthan, while other isolate shows high sequence similarity with CLCuV reported from Pakistan. The maximum similarity of first isolate, CLCuV-SG01, shows highest sequence identity with Cotton leaf curl Abohar (Rajasthan) virus, and second isolate, CLCuV-SG02, shows highest sequence identity with cotton leaf curl virus from Pakistan. Both isolates showed 85% similarities with each other. The sequence data revealed probable infiltration of some strains of Cotton leaf curl virus from Pakistan to India, or co-existence of different isolates under similar geographical conditions. While CLCuV-SG01 shows highest nt sequence similarity with CLCuV Rajasthan (Abohar), nt identity of V1 ORF (encoding coat protein) of SG01 shows the highest nt identity (100%) with CLCuV Multan (Bhatinda) and Abohar virus while AC1 region also showed difference. Complete nucleotide sequence of SG01 shows only 86% similarity with CLCuV Multan virus. Similarity search revealed significant difference in AV1 and AC1 regions with respect to DNA-A suggesting an evolutionary history of recombination. Computer based analysis, recombination detection Program (RDP) supports the recombination hypothesis, indicated that recombination with other begomoviruses had taken place within V1 ORF and AC1 ORF of CLCuV-SG01 and AC1 ORF of CLCuV-SG02 and also in noncoding intergenic region (IR).

Dominance of resistance-breaking cotton leaf curl Burewala virus (CLCuBuV) in northwestern India

“…It has been particularly devastating since 2009. Despite the severity of the disease, only a few cotton begomovirus sequences have been reported from India [27,[29][30][31][32], which is not enough to understand the emergence of the new and resistance-breaking strains of the virus. In the present study, CLCuD-affected cotton samples were collected from all major cotton-growing regions of northwestern India, and their variability was determined by cloning and analysis of the full-length Table 2 Origin of cotton leaf curl disease-associated begomoviruses isolates from northwestern India and features of the virus and betasatellites sequences.…”

“…After the first report of CLCuD in Sri Ganganagar, CLCuMuV, CLCuRV, and CLCuKoV were reported in all four major cotton-growing regions of India [29,31,32].…”

Three variants of cotton leaf curl begomoviruses with their satellite molecules are associated with cotton leaf curl disease aggravation in New Delhi

“…CLCuD is caused by whitefly transmitted monopartite begomoviruses in association with betasatellite and alphasatellite molecules (Briddon and Stanley 2006;Kumar et al 2010;Rajagopalan et al 2012). Betasatellites are a diverse group of circular ssDNA associated with CLCuD-begomovirus and essential for increased disease symptoms and in planta movement of virus (Saeed et al 2007).…”

“…Recombination is a significant driving force in the evolution of many begomoviruses (Padidam et al 1999). CLCuD-begomoviruses have been shown to have recombinant origin (Amrao et al 2010b;Kumar et al 2010;Sattar et al 2013). Evolution of recombinant betasatellite and their association with resistance breaking of CLCuD in cotton have also been reported (Amin et al 2006;Mansoor et al 2006;Amrao et al 2010b).…”

Emerging threats of begomoviruses to the cultivation of medicinal and aromatic crops and their management strategies

“…Genome of begomovirus is ss-circular DNA, either bipartite (DNA-A and DNA-B) or monopartite (DNA-A). In monopartite begomovirus all genes are present on the DNA-A molecule itself for replication while in bipartite begomoviruses Rep and CP gene are only present on DNA-A molecule and gene for movement MP and NSP are present on DNA-B [79,93]. The monopartite genome often assisted by satellite molecules betasatellite or alphasatellite.…”