Genetic variability of begomoviruses associated with cotton leaf curl disease originating from India.

Cotton leaf curl disease (CLCuD) causing viruses belong to the Begomovirus genus of the family Geminiviridae. Most begomoviruses are bipartite with two molecules of circular single stranded DNA (A and B) encapsidated in icosahedral geminate particles. However, the begomoviruses associated with CLCuD have DNA-beta instead of DNA-B. In this communication we report the complete genomic sequence of DNA-A component of two CLCuD-causing begomoviruses, cotton leaf curl Kokhran virus-Dabawali (CLCuKV-Dab), tomato leaf curl Bangalore virus-Cotton [Fatehabad] (ToLCBV-Cotton [Fat]) and partial sequences of two other isolates cotton leaf curl Rajasthan virus-Bangalore (CLCuRV-Ban) and cotton leaf curl Kokhran virus-Ganganagar (CLCuKV-Gang). A phylogenetic analysis of these isolates along with other related begomoviruses showed that ToLCBV-Cotton [Fat] isolate was closest to the tomato leaf curl Bangalore virus-5 (ToLCBV-Ban5) where as CLCuKV-Dab isolate was close to the cotton leaf curl Kokhran virus-Faisalabad1 (CLCuKV-Fai1), cotton leaf curl Kokhran virus-72b (CLCuKV-72b) and cotton leaf curl Kokhran virus-806b (CLCuKV-806b) isolates from Pakistan. The phylogenetic analysis further showed that the ToLCBV-Cotton [Fat] and CLCuKV-Dab isolates along with CLCuKV-Fai1, CLCuKV-72b and CLCuKV-806b are closer to the ToLCBV, tomato leaf curl Gujarat virus (ToLCGV), tomato leaf curl Gujarat virus-Varanasi (ToLCGV-Var) and tomato leaf curl Sri Lanka virus (ToLCSLV) isolates, where as cotton leaf curl Alabad virus-804a (CLCuAV-804a), cotton leaf curl Multhan virus (CLCuMV) cluster with the isolates from cotton leaf curl Rajasthan virus (CLCuRV) and okra yellow vein mosaic virus (OYVMV). These results demonstrate the extensive variability observed in this group of viruses. The AC4 ORF is the least conserved among these viruses. In order to further asses the variability in the CLCuD-causing begomoviruses, the region showing minimum similarity in the DNA-A sequence was first determined by a comparison of segments of different lengths of the aligned sequences. The results indicated that region 2411-424 (771 nt) was the least conserved. A phylogenetic tree constructed using the sequences of all the CLCuD causing begomoviruses, corresponding to the least conserved region showed that they form two distinct clusters.

Evidence for recombination among the tomato leaf curl virus strains/species from Bangalore, India.

Tomato leaf curl virus (ToLCV) belongs to the Begomovirus genus of the family Geminiviridae. These viruses have circular single stranded DNA molecules as their genome encapsidated in icosahedral geminate particles. Generally the Begomoviruses are bipartite with respect to their genomic composition. ToLCV from South India is unique in that only DNA A component has been isolated and sequenced thus far and there is no evidence for the presence of DNA B component. In this communication we report the genomic sequences of DNA A component of two strains of Tomato leaf curl Bangalore virus (ToLCBV), one from Bangalore, ToLCBV [Ban 5] and the other from Kolar (70 kms from Bangalore), ToLCBV [Kolar]. We have examined the possibility of recombination between strains/species that co-exist within the same geographical location. A novel method has been used to analyze the variation of ToLCV sequences reported from Bangalore and to assess the frequency and importance of recombinational events among the strains/species existing in Bangalore. The results indicate that there are potential sites of recombination in AV1, AV2, AC1 and intergenic regions of the viral genome and this accounts for the observed variability in these strains/species.