title: Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains.
abstract: In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.
authors.affiliation: School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.
authors.forename: Simona
authors.initials: S
authors.lastname: Kraberger
authors.affiliation: Virology Laboratory, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis, Tunisia. Electronic address: s.kumari@cgiar.org.
authors.forename: Safaa G
authors.initials: SG
authors.lastname: Kumari
authors.affiliation: Plant Pathology Research Program, Agricultural Research Corporation, P.O. Box 126, Wadmedani, Sudan.
authors.forename: Abdelmagid A
authors.initials: AA
authors.lastname: Hamed
authors.affiliation: Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Gronenborn
authors.affiliation: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia.
authors.forename: John E
authors.initials: JE
authors.lastname: Thomas
authors.affiliation: Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, QLD 4001, Australia.
authors.forename: Murray
authors.initials: M
authors.lastname: Sharman
authors.affiliation: South African National Bioinformatics Institute, SA Medical Research Unit for Bioinformatics Capacity Development, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa.
authors.forename: Gordon W
authors.initials: GW
authors.lastname: Harkins
authors.affiliation: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
authors.forename: Brejnev M
authors.initials: BM
authors.lastname: Muhire
authors.affiliation: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.affiliation: School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA. Electronic address: arvind.varsani@canterbury.ac.nz.
authors.forename: Arvind
authors.initials: A
authors.lastname: Varsani
mesh_terms: D029863:Cicer / Q000821:virology*; D004279:DNA, Viral / Q000235:genetics*; D017791:Geminiviridae / Q000145:classification* / Q000235:genetics; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000821:virology; D011995:Recombination, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013397:Sudan
chemical_list: D004279:DNA, Viral
keywords: Chickpea; Chickpea chlorotic dwarf virus; Geminivirus; Mastrevirus; Recombination; Sudan