title: 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.
authors.affiliation: Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Huma
authors.initials: H
authors.lastname: Saleem
authors.affiliation: Department of Bioinformatics and Biotechnology, GC University Faisalabad, Faisalabad, Pakistan.
authors.forename: Nazia
authors.initials: N
authors.lastname: Nahid
authors.affiliation: Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Sara
authors.initials: S
authors.lastname: Shakir
authors.affiliation: Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Sehrish
authors.initials: S
authors.lastname: Ijaz
authors.affiliation: Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Ghulam
authors.initials: G
authors.lastname: Murtaza
authors.affiliation: Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Asif Ali
authors.initials: AA
authors.lastname: Khan
authors.affiliation: Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Mubin
authors.affiliation: Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Muhammad Shah
authors.initials: MS
authors.lastname: Nawaz-Ul-Rehman
mesh_terms: D002681:China; D017791:Geminiviridae / Q000235:genetics*; D014644:Genetic Variation; D003368:Gossypium / Q000821:virology*; D007194:India; D009154:Mutation; D010154:Pakistan; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D011995:Recombination, Genetic