Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

Abstract

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton-infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombination detection programs and phylogenetic analyses showed that CLCuMuV and CLCuKoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.

Molecular diagnostic development for begomovirus-betasatellite complexes undergoing diversification: A case study

“…These virusesbetasatellites can occur in mixtures in the same host plant, and thus far include the begomoviral species and/or strains: Cotton leaf curl Alabad virus (CLCuAlV), Cotton leaf curl Bangalore virus (CLCuBaV), Cotton leaf curl Kokhran virus (CLCuKoV), Cotton leaf curl Multan virus (CLCuMuV). The predominant begomoviral pathogens of cotton in India and Pakistan are the CLCuKoV-Bu strain (second leaf curl disease outbreak) and CLCuMuV (first leaf curl disease outbreak) (Amrao et al, 2010;Briddon et al, 2001;2003b;Mubin et al 2010;Nawaz-ur-Rehman et al, 2012;Sartaj et al, 2014;Sattar et al, 2013;Saleem et al 2016;Zaffalon et al, 2011). In addition, several 'non-core' cotton leaf curl geminiviruses have been 5 found in mixed infection with the 'core leaf curl complex' Chickpea chlorotic dwarf virus (CpCDV) (also identified in tomato) (Ur-Rehman et al, 2015), Okra enation leaf curl virus (OEnLCV), Papaya leaf curl virus (PaLCV), Tomato leaf curl Bangalore virus (ToLCBaV), and Tomato leaf curl New Delhi virus (ToLCNDV) (Saeed, 2010).…”

Evolutionary ecology of virus emergence

“…Given the role of geminivirus coat proteins in intraplant movement and between‐plant vector transmission, it should not come as a surprise that the protein is linked to an emergence episode . Similar recombination‐mediated emergence events may have occurred in other geminiviruses, including EACMV emergence in Cameroon, tomato yellow leaf curl emergence in Spain and the Mediterranean basin, cotton leaf curl virus in Pakistan, and sugarcane yellow leaf virus in Hawaii …”

Distribution of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Mitotypes in Commercial Cotton Fields in the Punjab Province of Pakistan

“…The differences in genetic diversity are reflective of the dynamic patterns of diversification, which has been shown to influence mitotype distribution. Accordingly, when certain mitotypes show differences in transmission competency over others, the distribution and spread of cotton leaf curl disease-begomoviruses in cotton and vegetable crops can be altered dramatically, or result in the emergence of previously unrecognized species or strains, often due to recombination (Bisaro 1994;Brown 2001;Fauquet et al 2005;Saleem et al 2016).…”

“…In Pakistan and India, over 60 begomoviral species or strains have been described from cultivated and wild plant species (Ho et al 2017). Cotton leaf curl disease is caused by one of several monopartite begomoviruses or strains, and associated betasatellites that are endemic to much of southern Asia, including Pakistan (Zhou et al 1998;Saleem et al 2016). During the past several decades, the emergence of cotton leaf curl disease has resulted in major economic losses in the cotton producing areas of Pakistan (Briddon et al 2001;Zubair et al 2017).…”