Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species

Abstract

Cacao swollen shoot virus is a member of the family Caulimoviridae, genus Badnavirus and is naturally transmitted to Theobroma cacao (L.) by several mealybug species. CSSV populations in West African countries are highly variable and genetically structured into several different groups based on the diversity in the first part of ORF3 which encodes the movement protein. To unravel the extent of isolate diversity and address the problems of low titer and mixed viral sequences in samples, we used Illumina MiSeq and HiSeq technology. We were able to reconstruct de novo 20 new complete genomes from cacao samples collected in the Cocoa Research Institute of Ghana (CRIG) Museum and from the field samples collected in Côte d'Ivoire or Ghana. Based on the 20% threshold of nucleotide divergence in the reverse transcriptase/ribonuclease H (RT/RNase H) region which denotes species demarcation, we conclude there exist seven new species associated with the cacao swollen shoot disease. These new species along with the three already described leads to ten, the total number of the complex of viral species associated with the disease. A sample from Sri Lanka exhibiting similar leaf symptomology to West African CSSD-affected plants was also included in the study and the corresponding sequence represents the genome of a new virus named cacao bacilliform SriLanka virus (CBSLV).

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

“…These large-scale studies assess the spatial and temporal distribution of plant virus populations within specific ecosystems, helping deciphering key components of viral evolution and disease emergence that shape wild and cultivated habitats in important agro-ecological interfaces (Alexander et al, 2014). In addition, some of the HTS-based approaches allow for full genome assembly, facilitating genome-wide studies (De Souza et al, 2017; Hily et al, 2018a; Muller et al, 2018), which were rarely feasible during the Sanger-sequencing era. Finally, RNA seq-based techniques can provide comprehensive transcriptomic analyses enabling the evaluation of gene expression between different phenological stages or varieties (Zenoni et al, 2010; Massonnet et al, 2017), the monitoring responses to environmental constraints (such as drought, temperature) (Haider et al, 2017; Londo et al, 2018) or the study of plant responses to specific infectious agent (Gambino et al, 2012; Blanco-Ulate et al, 2015).…”

Characterization and genetic diversity of Dioscorea bacilliform viruses present in a Pacific yam germplasm collection

“…A pipeline similar to that described in Muller et al . () was used for the processing of NGS data and characterization of badnavirus diversity. Raw reads were trimmed to obtain optimum quality using the dynamic trim function of S olexa QA ++ v. 3.1.3 (Cox et al .…”

“…Undigested RCA products of 10 Papua New Guinea (PNG) samples Quality of the raw reads was assessed with FastQC v. 0.10.1 (Babraham Bioinformatics). A pipeline similar to that described in Muller et al (2018) was used for the processing of NGS data and characterization of badnavirus diversity. Raw reads were trimmed to obtain optimum quality using the dynamic trim function of…”

Management of the Cacao Swollen Shoot Virus (CSSV) Menace in Ghana: The Past, Present and the Future

“…Recent molecular studies with the use of advance sequencing methods such Next generation tools have provided the opportunity to further classify CSSV isolates across the West African sub-region into new groups based on their molecular information at the DNA level. Some of these studies have identified wide variability in the strains of the virus and virulence of the disease in new infections especially in the Western region of Ghana [3,19,20] CSSV is semi-persistently transmitted by several species of mealybugs (Pseudococcidae, Homoptera) on cocoa [21,22]. The vectors feed on all parts of the cocoa tree including flowers, cherelles, pods and leaves.…”

“…The cacao swollen shoot virus disease (CSSVD) which is considered the most economically important cocoa virus disease could account for 15-50% yield loss if the severe strains are involved in infections [2,3]. Since the discovery of this important disease in Ghana, it has been managed through the "cutting out and replanting system" with the aim of removing sources of inoculum from affected cocoa plantations and replanting with tolerant cocoa hybrids [3][4][5]. Nonetheless, reports from many reassessments and disease surveys indicate that the prevalence of the disease is still high with varying virulence across the cocoa regions.…”