Diversity and recombination analysis of Cotton leaf curl Multan betasatellite associated with cotton leaf curl begomovirus disease complex

Betasatellites are single-stranded DNA molecules associated with most monopartite begomoviruses of family Geminiviridae. They are symptoms modulating molecules and depend on their helper viruses for replication, encapsidation and movement. To investigate the genetic diversity of cotton leaf curl Multan betasatellite (CLCuMuB), different Pakistani isolates of betasatellites were retrieved from the NCBI data bank. The sequences were compared to all available sequences of CLCuMuB in the database, identified from cotton in Pakistan, India and China. Phylogenetic and recombination analysis showed the sequences are separated into five major groups. This is primarily based on recombination within the satellite conserved region (SCR) of the betasatellite genome. The first group consists of sequences of the original betasatellite associated with the first epidemic of cotton leaf curl disease (CLCuD) in the 1990s, while the second group consists of recombinant betasatellites associated with the second epidemic of CLCuD, containing a short fragment of tomato leaf curl betasatellite (ToLCB) DNA in the satellite conserved region (SCR). The third group contains a short fragment of papaya leaf curl betasatellite (PaLCuB), while the fourth group contains a short fragment of tobacco curly shoot betasatellite (TbCSB) in the SCR region. The fifth group consists of sequences of betasatellite associated with the recent begomovirus disease complex identified from Vehari. This betasatellite contains a short fragment of sequences in the SCR region of a defective betasatellite (KT228331) from India. This new strain of CLCuMuB is named CLCuMuB(Veh). Here, the significance of the evolution of CLCuMuB with respect to the CLCuD complex is discussed.

Automated summary

The study investigates the genetic diversity of cotton leaf curl Multan betasatellite (CLCuMuB) by analyzing different Pakistani isolates of betasatellites, revealing recombination within the genome and dividing the sequences into five major groups associated with different epidemics of cotton leaf curl disease. The findings shed light on the evolution of CLCuMuB and its significance in the CLCuD complex.