Distribution of cotton leaf curl virus species/strain and characterization of associated satellite molecules in Gossypium hirsutum

Cotton leaf curl disease (CLCuD) is a major threat to cotton production throughout the world. In the present study, cotton crop in the South-Western districts of Punjab was monitored and surveyed for CLCuD. Begomoviruses and associated betasatellites and alphasatellites found in infected cotton plants with the CLCuD complex were sequenced partially. Here, we studied ten partial sequences for the characterization of CLCuD complex. Pairwise sequence analysis revealed that CLCuD-begomovirus isolates from Mansa is a close relative of cotton leaf curl Multan virus (CLCuMuV) while isolates from Bathinda and Abohar are members of CLCuMuV-Rajasthan strain. The betasatellite isolates characterized in this study shared 58.8–87.6% nt sequence homology with each other and showed maximum nucleotide sequence identity with cotton leaf curl Multan betasatellite (CLCuMuB). The alphasatellite isolates from Bakainwala and Muktsar showed maximum nt identity with cotton leaf curl Multan alphasatellite (CLCuMuA) and Gossypium darwani symptomless alphasatellite (GDrSLA) respectively.