title: Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton.
abstract: The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990's but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These viruses were also cloned and sequenced through Sanger sequencing to confirm the identity of the begomoviruses and that all clones possessed a full complement of the TrAP gene. A new strain of betasatellite was identified here and named CLCuMuBVeh. The implications of these findings in efforts to control CLCuD are discussed.
authors.affiliation: National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.|Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Zubair
authors.affiliation: National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.|Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
authors.forename: Syed Shan-E-Ali
authors.identifier: http://orcid.org/0000-0002-2976-4624
authors.initials: SS
authors.lastname: Zaidi
authors.affiliation: Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
authors.forename: Sara
authors.initials: S
authors.lastname: Shakir
authors.affiliation: National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Farooq
authors.affiliation: National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
authors.forename: Imran
authors.initials: I
authors.lastname: Amin
authors.affiliation: USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA.
authors.forename: Jodi A
authors.initials: JA
authors.lastname: Scheffler
authors.affiliation: USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA.
authors.forename: Brian E
authors.identifier: http://orcid.org/0000-0003-1968-8952
authors.initials: BE
authors.lastname: Scheffler
authors.affiliation: National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan. Shahidmansoor7@gmail.com.
authors.forename: Shahid
authors.initials: S
authors.lastname: Mansoor
mesh_terms: D053839:Begomovirus / Q000145:classification* / Q000235:genetics*; D004276:DNA, Satellite; D004279:DNA, Viral; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D003368:Gossypium / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing; D016366:Open Reading Frames; D010154:Pakistan; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D018515:Plant Leaves / Q000821:virology; D011995:Recombination, Genetic
chemical_list: D004276:DNA, Satellite; D004279:DNA, Viral