New strains of chickpea chlorotic dwarf virus discovered on diseased papaya and tomato plants in Burkina Faso

Abstract

This is the first description of full genome sequences of chickpea chlorotic dwarf virus (CpCDV; genus Mastrevirus; family Geminiviridae) identified in papaya and tomato plants sampled in Burkina Faso. The CpCDV full genome sequences from papaya and tomato share the highest pairwise sequence identity (84% and 93.5%) with Sudanese isolates of the CpCDV-K and CpCDV-M strains, respectively. Based on the strain demarcation threshold (>94% identity) for mastreviruses, we propose two new strains, CpCDV-Q and CpCDV-R, identified in papaya and tomato, respectively. Phylogenetic analysis confirmed that the sequences belong to a distinct clade of the highly diverse population of CpCDVs. Evidence of inter-strain recombination provided more support for the important role of recombination in CpCDV evolution. The discovery of CpCDV on papaya, a previously unsuspected host, raises many questions about the natural and potential host range of this dicot-infecting mastrevirus species that is reported to be emerging worldwide.

Deep Sequencing Data and Infectivity Assays Indicate that Chickpea Chlorotic Dwarf Virus is the Etiological Agent of the “Hard Fruit Syndrome” of Watermelon

“…Beside chickpea ( Cicer aretinum ), where it was originally described [ 4 ], several pulse crops, staple food for millions of people, have been found infected by CpCDV, such as faba bean ( Vicia faba ), lentil ( Lens culinaris ), bean ( Phaseolus vulgaris ) and wild legume species ( Accasia spp. Cajanus cajan , Dolichus lablab , Rinchosia minima ) in Sudan [ 5 ]; CpCDV was also detected in Beta vulgaris in Iran [ 6 ], in papaya ( Carica papaya ) in Burkina Faso [ 7 ], in some economically important Solanaceae such as pepper ( Capsicum annuum ) in Oman [ 8 ], and tomato ( Lycopersicon esculentum ) in Pakistan and Burkina Faso [ 7 , 9 ], in Malvaceae as okra ( Abelmoschus esculentus ) in Pakistan [ 10 ], and cotton ( Gossypium hirsutum ) in India [ 11 ]. CpCDV infects also other cucurbits beside watermelon [ 2 ], including squash ( Cucurbita pepo ) in Egypt [ 12 ] and cucumber ( Cucumis sativus ) in Pakistan [ 13 ].…”

Viruses and Phytoparasitic Nematodes of Cicer arietinum L.: Biotechnological Approaches in Interaction Studies and for Sustainable Control

“…In recent years, the most invasive chickpea virus has been CpCDV. This virus, first reported in India in 1993 (Horn et al, 1993 ), has recently spread in many countries and among several crops, including other leguminous species (faba bean, lentil, bean), some solanaceous (tomato, pepper) and cucurbits (squash, cucumber), as well as other unrelated species such as cotton, sugar beet, okra, and papaya (Manzoor et al, 2014 ; Fahmy et al, 2015 ; Kraberger et al, 2015 ; Ouattara et al, 2017 ). In a newly discovered disease of watermelon in Tunisia, causing fruit hardness, CpCDV has been found as the causal agent (Zaagueri et al, 2017a , b ).…”

Complete Genome Sequence of a New Chickpea Chlorotic Dwarf Virus Strain Isolated from Tomato in Kenya, Obtained from Illumina Sequencing

“…Seven Mastrevirus species infect dicotyledonous plants, including Chickpea chlorotic dwarf virus (CpCDV) (3)(4)(5)(6)(7)(8)(9). Nineteen CpCDV strains (strains A to S) have been described (9)(10)(11), but the presence of the virus in East Africa has not yet been reported. In this study, we identified a novel CpCDV strain, infecting tomato in Kenya, through metagenomic sequencing and phylogenetic analysis.…”

“…De novo genome assembly yielded two contigs; one was 2,469 nucleotides long, with a GϩC content of 51.73%, and the other was Ͻ138 bp long. A BLASTN-based search revealed both contigs to represent CpCDV, with the larger contig sharing the highest nucleotide similarity (88.7%) with the complete circular genome sequences of two CpCDV strains infecting tomato in Burkina Faso (GenBank accession numbers KY047532 and KY047533) (11). Four ORFs, typical of Mastrevirus sp.…”