Cacao sustainability: The case of cacao swollen-shoot virus co-infection

The cacao swollen shoot virus disease (CSSVD) is among the most economically damaging diseases of cacao trees and accounts for almost 15-50% of harvest losses in Ghana. This virus is transmitted by several species of mealybugs (Pseudococcidae, Homoptera) when they feed on cacao plants. One of the mitigation strategies for CSSVD investigated at the Cocoa Research Institute of Ghana (CRIG) is the use of mild-strain cross-protection of cacao trees against the effects of severe strains. In this study, simple deterministic, delay, and stochastic ordinary differential equation-based models to describe the dynamic of the disease and spread of the virus are suggested. Model parameters are estimated using detailed empirical data from CRIG. The modeling outcomes demonstrate a remarkable resemblance between real and simulated dynamics. We have found that models with delay approximate the data better and this agrees with the knowledge that CSSVD epidemics develop slowly. Also, since there are large variations in the data, stochastic models lead to better results. We show that these models can be used to gain useful informative insights about the nature of disease spread.

The P2 nucleic acid binding protein of Sugarcane bacilliform virus is a viral pathogenic factor

Background

Saccharum spp. is the primary source of sugar and plays a significant role in global renewable bioenergy. Sugarcane bacilliform virus (SCBV) is one of the most important viruses infecting sugarcane, causing severe yield losses and quality degradation. It is of great significance to reveal the pathogenesis of SCBV and resistance breeding. However, little is known about the viral virulence factors or RNA silencing suppressors and the molecular mechanism of pathogenesis.

Methods

To systematically investigate the functions of the unknown protein P2 encoded by SCBV ORF2. Phylogenetic analysis was implemented to infer the evolutionary relationship between the P2 of SCBV and other badnaviruses. The precise subcellular localization of P2 was verified in the transient infiltrated Nicotiana benthamiana epidermal mesophyll cells and protoplasts using the Laser scanning confocal microscope (LSCM). The post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) RNA silencing suppressor activity of P2 was analyzed, respectively. Furthermore, restriction digestion and RT-qPCR assays were conducted to verify the probable mechanism of P2 on repressing DNA methylation. To explore the pathogenicity of P2, a potato virus X-based viral vector was used to heterologously express SCBV P2 and the consequent H2O2 accumulation was detected by the 3,3'-diaminobenzidine (DAB) staining method.

Results

Phylogenetic analysis shows that SCBV has no obvious sequence similarity and low genetic relatedness to Badnavirus and Tungrovirus representatives. LSCM studies show that P2 is localized in both the cytoplasm and nucleus. Moreover, P2 is shown to be a suppressor of PTGS and TGS, which can not only repress ssRNA-induced gene silencing but also disrupt the host RNA-directed DNA methylation (RdDM) pathway. In addition, P2 can trigger an oxidative burst and cause typical hypersensitive-like response (HLR) necrosis in systemic leaves of N. benthamiana when expressed by PVX. Overall, our results laid a foundation for deciphering the molecular mechanism of SCBV pathogenesis and made progress for resistance breeding.

Diverse Novel Viruses Coinfecting the Tropical Ornamental Plant Polyscias balfouriana in China

The viromic profile of Polyscias balfouriana cv. Marginata, a perennial woody and ornamental plant, was determined using ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) sequencing. Five viruses (i.e., polyscias mosaic virus, PoMV; one potential novel rhabdovirus; and three novel viruses of Betaflexiviridae and Closteroviridae) were detected and prevalence-surveyed in Hainan province, China. The genomes of polyscias capillovirus 1 (PCaV-1) and polyscias citrivirus 1 (PCiV-1) of family Betaflexiviridae were completed, and the genomes of polyscias crinivirus 1 (PCrV-1) of Closteroviridae were nearly completed lacking the 5′ and 3′ termini. PCaV-1 shares 68% genome nucleotide (nt) identity and 66% replicase (Rep) amino acid (aa) identity with homologues in apple stem grooving virus (ASGV). PCiV-1 shares 65% genome nt identity and 64% Rep aa identity with homologs in citrus leaf blotch virus (CLBV). Meeting the species demarcation criteria, PCaV-1 and PCiV-1 were considered to be new species in genera Capillovirus and Citrivirus, respectively. PCrV-1 shares high genome nt identity (62%), heat shock protein 70-like protein (HSP70h) and RNA-dependent RNA polymerase (RdRp) aa identity (78−80%) with homologues in tomato chlorosis virus (ToCV). We tentatively consider PCrV-1 to be an unclassified member of the Crinivirus genus. PoMV, PCaV-1, PCiV-1, and PCrV-1 are the prevalent viruses with >73% occurrence in the Xinglong Tropical Botanical Garden, Hainan, China.

Grapevine vein clearing virus Is Prevalent and Genetically Variable in Grape Aphid (Aphis illinoisensis Shimer) Populations

Grapevine vein clearing virus (GVCV) causes severe stunting and death of cultivated grapevines and is prevalent in native Vitis spp. and Ampelopsis cordata in the Midwest region of the United States. GVCV can be transmitted from wild A. cordata to Vitis spp. by grape aphid (Aphis illinoisensis) under greenhouse conditions, but its prevalence, genetic composition, and genome number in native grape aphids are unknown. In this study, we collected grape aphids from native Vitaceae across the state of Missouri in 2018 and 2019, and conducted diagnostic, genetic, and quantitative analyses. GVCV was detected in 91 of the 105 randomly sampled communities on 71 Vitaceae plants (87%). It was present in 211 of 525 single grape aphids (40%). Diverse GVCV variants from aphids were present on both GVCV-negative and GVCV-positive plants. Identical GVCV variants were found in grape aphids sampled from wild and cultivated Vitaceae, indicating that viruliferous aphids likely migrate and disperse GVCV variants among wild and cultivated Vitaceae. In addition, we found that the number of GVCV genomes varies largely in the stylet and body of individual aphids. Our study provides a snapshot of GVCV epidemics and genetic structure in its mobile vector and sessile hosts. This presents a good model for studying the epidemiology, ecology, and evolution of a plant virus.

A Fig Deal: A Global Look at Fig Mosaic Disease and its Putative Associates

Fig mosaic disease (FMD) is a complex viral disease with which 12 viruses, including a confirmed causal agent, fig mosaic emaravirus (FMV), and three viroids are associated worldwide. FMD was first described in California in the early 1930s. Symptoms include foliar chlorosis, deformation, and mosaic patterns. FMD is disseminated by vegetative propagation, seed transmission, and vectors, including a mite, Aceria ficus. Management of the disease in fig orchards relies on scouting and elimination of infected trees. In this review, we focus on the distribution of the FMD-associated viruses and viroids by summarizing worldwide surveys and their genome structure. We also determined the full-length sequence of FMV and fig badnavirus 1 (FBV-1) isolates from Connecticut and compared the virus and viroid sequences from fig isolates. We suggest important areas of research including determining the potential synergistic effect of multiple viruses, elucidating the full-length genome sequence of each associated virus, and relating virus titer to phenotypic changes in Ficus carica.

North American Grape 'Norton' is Resistant to Grapevine Vein Clearing Virus

Grapevines (Vitis spp.) host viruses belonging to 17 families. Virus-associated diseases are a constant challenge to grape production. Genetic resources for breeding virus-resistant grape cultivars are scarce. 'Norton' is a hybrid grape of North American Vitis aestivalis and is resistant to powdery mildew and downy mildew. In this study, we assessed resistance of 'Norton' to grapevine vein clearing virus (GVCV), which is prevalent in native, wild Vitaceae and in vineyards in the Midwest region of the U.S. We did not detect GVCV in 'Norton' as either the scion or the rootstock up to 3 years after it was grafted with a GVCV-infected 'Chardonel' grapevine. Upon sequencing of small RNAs, we were able to assemble the GVCV genome from virus small RNAs in GVCV-infected 'Chardonel' scion or rootstock, but not from grafted 'Norton' scion and rootstock. This study unveils a new trait of 'Norton' that can be used in breeding GVCV-resistant grape cultivars, and to investigate genetic mechanisms of 'Norton' resistance to GVCV.