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, A. A.; Gronenborn, Bruno; Thomas, J. E.; Sharman, Murray; Harkins, Gordon William; Muhire, Brejnev; Martin, Darren P.; Varsani, Arvind

doi:10.1016/j.meegid.2014.11.024

Cited by 23 publications

(28 citation statements)

References 55 publications

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“…As previously shown (Kraberger et al , ), recombination analyses using rdp revealed that recombinations have occurred during the evolution of the F strain. The analyses showed that the Iranian strain F isolates, like other isolates belonging to CpCDV‐F 1‐I , have evidence of recombination with CpCDV‐A‐like and CpCDV‐G isolates as potential major and minor parents, respectively ( P = 1.46 × 10 −7 ), with a rep / repA fragment of approximately 0.6 kb transferred by the recombination (recombination event 20; Kraberger et al , ).…”

Section: Resultssupporting

confidence: 66%

“…Merges of CpCDV strains have previously been proposed (Kraberger et al , ). In the case of the proposed merging of the strains CpCDV‐F and CpCDV‐G, the pairwise comparisons (Fig. )…”

Section: Resultsmentioning

confidence: 99%

“…The Iranian CpCDV isolates were closely related either to other isolates of CpCDV‐A from Syria, Tunisia and Turkey or to isolates of CpCDV‐F from Yemen, Pakistan and Syria. Recently, CpCDV strains have been classified into genotypes and variants with a threshold of 94–97% and >99% pairwise identity, respectively (Kraberger et al , ). Using this classification, CpCDV‐F isolates studied here grouped into the genotype and variant of CpCDV‐F 1‐I and CpCDV‐A isolates along with all other previously reported strain A isolates grouped into the single assigned genotype and variant of CpCDV‐A 1‐I .…”

Section: Resultsmentioning

confidence: 99%

“…), while for some strains (CpCDV‐C, ‐K, ‐N, ‐O and ‐P), complete genome sequences were needed for final classification. Further classification of CpCDV‐F into genotypes and variants (Kraberger et al , ) was supported only with the phylogenetic tree for the rep gene, and not supported when using the cp and mp genes. For example, the classification of the CpCDV isolates from Oman and Sudan as CpCDV‐F 1‐II and CpCDV‐F 2‐I , respectively (Kraberger et al , ), was supported only in the analysis of the rep gene.…”

Section: Resultsmentioning

confidence: 99%

“…Recombination among CpCDV isolates was analysed using rdp 4 (Martin et al , ) as described by Kraberger et al ().…”

Section: Methodsmentioning

confidence: 99%

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Diversity and occurrence of chickpea chlorotic dwarf virus on legumes from Iran

et al. 2019

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Chickpea chlorotic dwarf virus (CpCDV; genus Mastrevirus, family Geminiviridae) is one of the most important legume‐infecting viruses with a wide host range and geographic distribution in Africa and Asia. In Iran, CpCDV is common in chickpea (Cicer arietinum), but there is limited information about diversity and infections in plants of other legume species. In the current study, a total of 1671 leaf samples from different pulse crops with symptoms were collected in nine provinces of Iran, and the CpCDV infection status was tested by PCR and/or rolling circle amplification (RCA), resulting in the detection of CpCDV in samples of chickpea, lentil (Lens culinaris) and faba bean (Vicia faba) from different regions. Sequence analysis of complete genomes of 18 isolates recovered by digestion of RCA products revealed infection with isolates of the strains CpCDV‐A and CpCDV‐F in chickpea, lentil and faba bean. Phylogenetic analysis showed that the Iranian isolates of CpCDV were closely related to previously sequenced isolates of CpCDV‐A and CpCDV‐F. To the authors' knowledge, this is the first report of CpCDV‐F in Iran. Using agroinoculation with infectious clones for one isolate each of CpCDV‐A and CpCDV‐F, infectivity was confirmed in both faba bean and chickpea, with plants developing leaf curling and/or yellowing. Both infectious clones also successfully infected Nicotiana benthamiana resulting in mild yellowing and intensive leaf curling for CpCDV‐A, and dark‐green mosaic, dwarfing and mild leaf curling for CpCDV‐F.

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Section: Resultssupporting

confidence: 66%

“…Merges of CpCDV strains have previously been proposed (Kraberger et al , ). In the case of the proposed merging of the strains CpCDV‐F and CpCDV‐G, the pairwise comparisons (Fig. )…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…Recombination among CpCDV isolates was analysed using rdp 4 (Martin et al , ) as described by Kraberger et al ().…”

Section: Methodsmentioning

confidence: 99%

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