Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination - a driving force in the emergence of new strains

Simona Kraberger, Safaa G. Kumari, Abdelmagid A. Hamed, Bruno Gronenborn, John E. Thomas, Murray Sharman, Gordon W. Harkins, Brejnev M. Muhire, Darren P. Martin, Arvind Varsani

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)203-215
Number of pages13
JournalInfection, Genetics and Evolution
Volume29
DOIs
StatePublished - Jan 1 2015
Externally publishedYes

Fingerprint

Chickpea chlorotic dwarf virus
Geminiviridae
Cicer
Sudan
Genetic Recombination
recombination
virus
Viruses
Eastern Africa
Middle East
Genetic Selection
Mastrevirus
natural selection
Open Reading Frames
genome
pathogen
Genome
protein
Infection
rate

Keywords

  • Chickpea
  • Chickpea chlorotic dwarf virus
  • Geminivirus
  • Mastrevirus
  • Recombination
  • Sudan

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Molecular Biology
  • Microbiology
  • Infectious Diseases
  • Microbiology (medical)
  • Medicine(all)

Cite this

Molecular diversity of Chickpea chlorotic dwarf virus in Sudan : High rates of intra-species recombination - a driving force in the emergence of new strains. / Kraberger, Simona; Kumari, Safaa G.; Hamed, Abdelmagid A.; Gronenborn, Bruno; Thomas, John E.; Sharman, Murray; Harkins, Gordon W.; Muhire, Brejnev M.; Martin, Darren P.; Varsani, Arvind.

In: Infection, Genetics and Evolution, Vol. 29, 01.01.2015, p. 203-215.

Research output: Contribution to journalArticle

Kraberger, Simona ; Kumari, Safaa G. ; Hamed, Abdelmagid A. ; Gronenborn, Bruno ; Thomas, John E. ; Sharman, Murray ; Harkins, Gordon W. ; Muhire, Brejnev M. ; Martin, Darren P. ; Varsani, Arvind. / Molecular diversity of Chickpea chlorotic dwarf virus in Sudan : High rates of intra-species recombination - a driving force in the emergence of new strains. In: Infection, Genetics and Evolution. 2015 ; Vol. 29. pp. 203-215.
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