Search

Pawpaw (Asimina triloba) trees exhibiting stunting and foliar mosaic, chlorosis, or distortions were observed in New York. In 2021, leaf samples from two symptomatic trees and a sapling, as well as two asymptomatic trees, were tested for the presence of viruses and viroids by high-throughput sequencing (HTS) using total RNA after ribosomal RNA depletion. HTS sequence information revealed tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) in symptomatic but not in asymptomatic leaves. HTS reads and de novo-assembled contigs covering the genomes of both viruses were obtained, with a higher average read depth for RNA2 than RNA1. The occurrence of TRSV and ToRSV was confirmed in the original leaf samples used for HTS and 12 additional trees and saplings from New York and Maryland in 2022 by RT-PCR combined with Sanger sequencing, and DAS-ELISA. Single infections by TRSV in 11 of 14 trees and dual infections by TRSV and ToRSV in 3 of 14 trees were identified. The nucleotide sequence identity of partial gene fragments of TRSV and ToRSV was high among pawpaw isolates (94.9-100% and 91.8-100%, respectively) and between pawpaw isolates and isolates from other horticultural crops (93.6-100% and 71.3-99.3%, respectively). This study is the first to determine the virome of pawpaw.

[EN] The stone fruit genus Prunus, within the family Rosaceae, comprises more than 230 species, some of which have great importance or value as ornamental or fruit crops. Prunus are affected by numerous viruses and viroids linked to the vegetative propagation practices in many of the cultivated species. To date, 44 viruses and three viroids have been described in the 9 main cultivated Prunus species. Seven of these viruses and one viroid have been identified in Prunus hosts within the last 5 years. This work addresses recent advances and prospects in the study of viruses and viroids affecting Prunus species, mostly concerning the detection and characterisation of the agents involved, pathogenesis analysis and the search for new control tools. New sequencing technologies are quickly reshaping the way we can identify and characterise new plant viruses and isolates. Specific efforts aimed at virus identification or data mining of high-throughput sequencing data generated for plant genomics-oriented purposes can efficiently reveal the presence of known or novel viruses. These technologies have also been used to gain a deeper knowledge of the pathogenesis mechanisms at the gene and miRNA expression level that underlie the interactions between Prunus spp. and their main viruses and viroids. New biotechnological control tools include the transfer of resistance by grafting, the use of new sources of resistance and the development of gene silencing strategies using genetic transformation. In addition, the application of next generation sequencing and genome editing techniques will contribute to improving our knowledge of virus¿host interactions and the mechanisms of resistance. This should be of great interest in the search to obtain new Prunus cultivars capable of dealing both with known viruses and viroids and with those that are yet to be discovered in the uncertain scenario of climate change.

[EN] The stone fruit genus Prunus, within the family Rosaceae, comprises more than 230 species, some of which have great importance or value as ornamental or fruit crops. Prunus are affected by numerous viruses and viroids linked to the vegetative propagation practices in many of the cultivated species. To date, 44 viruses and three viroids have been described in the 9 main cultivated Prunus species. Seven of these viruses and one viroid have been identified in Prunus hosts within the last 5 years. This work addresses recent advances and prospects in the study of viruses and viroids affecting Prunus species, mostly concerning the detection and characterisation of the agents involved, pathogenesis analysis and the search for new control tools. New sequencing technologies are quickly reshaping the way we can identify and characterise new plant viruses and isolates. Specific efforts aimed at virus identification or data mining of high-throughput sequencing data generated for plant genomics-oriented purposes can efficiently reveal the presence of known or novel viruses. These technologies have also been used to gain a deeper knowledge of the pathogenesis mechanisms at the gene and miRNA expression level that underlie the interactions between Prunus spp. and their main viruses and viroids. New biotechnological control tools include the transfer of resistance by grafting, the use of new sources of resistance and the development of gene silencing strategies using genetic transformation. In addition, the application of next generation sequencing and genome editing techniques will contribute to improving our knowledge of virus¿host interactions and the mechanisms of resistance. This should be of great interest in the search to obtain new Prunus cultivars capable of dealing both with known viruses and viroids and with those that are yet to be discovered in the uncertain scenario of climate change.

BackgroundGenome-wide association study (GWAS) is a useful tool for detecting and characterizing traits of interest including those associated with disease resistance in soybean. The availability of 50,000 single nucleotide polymorphism (SNP) markers (SoySNP50K iSelect BeadChip; www.soybase.org ) on 19,652 soybean and wild soybean plant introductions (PIs) in the USDA Soybean Germplasm Collection allows for fast and robust identification of loci associated with a desired phenotype. By using a genome-wide marker set to predict phenotypic values, genomic prediction for phenotype-unknown but genotype-determined PIs has become possible. The goal of this study was to describe the genetic architecture associated with sensitivity to Tobacco ringspot virus (TRSV) infection in the USDA Soybean Germplasm Collection.ResultsTRSV-induced disease sensitivities of the 697 soybean PIs were rated on a one to five scale with plants rated as one exhibiting mild symptoms and plants rated as five displaying terminal bud necrosis (i.e., bud blight). The GWAS identified a single locus on soybean chromosome 2 strongly associated with TRSV sensitivity. Cross-validation showed a correlation of 0.55 (P < 0.01) to TRSV sensitivity without including the most significant SNP marker from the GWAS as a covariate, which was a better estimation compared to the mean separation by using significant SNPs. The genomic estimated breeding values for the remaining 18,955 unscreened soybean PIs in the USDA Soybean Germplasm Collection were obtained using the GAPIT R package. To evaluate the prediction accuracy, an additional 55 soybean accessions were evaluated for sensitivity to TRSV, which resulted in a correlation of 0.67 (P < 0.01) between actual and predicted severities.ConclusionA single locus responsible for TRSV sensitivity in soybean was identified on chromosome 2. Two leucine-rich repeat receptor-like kinase genes were located near the locus and may control sensitivity of soybean to TRSV inf

The Panel on Plant Health performed a pest categorisation of Cherry leafroll virus (CLRV) for the European Union (EU) territory. CLRV is a well-defined virus species of the genus Nepovirus, for which the entire genome sequence and molecular detection assays are available. CLRV is transmitted by vegetative multiplication of infected hosts and is also seed- and pollen-transmitted (both horizontally and vertically) in many of its hosts. There is, however, evidence that interspecific transmission by the pollen-mediated mechanism is very limited. CLRV has a wide host range, which contains both woody and herbaceous hosts, many of which are largely present in natural environments. It is listed on plants of Rubus spp. for planting in Annex IIAI of Directive 2000/29/EC. CLRV is widely present in the EU but there are very few records on its regulated hosts. It is not expected to be affected by ecoclimatic conditions wherever its hosts are present and has the potential to establish in large parts of the EU territory. CLRV can spread through efficient seed- and pollen-mediated transmission mechanisms and through the movement of vegetatively propagated plants for planting of numerous hosts. However, the existence of efficient and widely adopted certification systems for some of these hosts constitutes a limitation to CLRV spread. Although the virus alone or when in mixed infection can cause significant disease in some hosts, the actual impact of CLRV is very difficult to evaluate but generally appears to be limited.

So far, only limited research has been carried out on viruses infecting raspberry, even though the diseases that these viruses cause result in economical losses for raspberry growers. Raspberry ringspot virus (RpRSV) belongs to the family Comoviridae and the genus Nepovirus. Nepoviruses are characterized by their icosahedral virus particles and bipartite genome of single-stranded (+) RNA (RNA-1 and RNA-2). These viruses are transmitted mainly by nematodes of the genus Longidorus, which feed on the roots of plants. RpRSV causes disease in raspberry, grapevine, strawberry and many other plants. The aim of this project was to confirm infection of RpRSV in raspberry samples from Belarus by amplification and sequencing of the coat protein gene. The aim was also to characterize the detected viruses in the samples, since there is little knowledge about nepoviruses in raspberry. RNA was extracted from raspberry stem tissue and cDNA was synthesized by reverse transcription with random primers. The cDNA samples were then used for PCR with different RpRSV-specific primers, in order to amplify parts of the RNA-2 component. However, there was no success in amplification of RpRSV RNA-2 for any of the primer pairs tested. Changing annealing temperature and reagent mixture composition did not improve the results. It is hypothesized that this can be due to sequence differences between these RpRSV isolates and previously studied isolates that prevent the primers from binding. However, more extensive analyses are needed to be able to make any reliable conclusions

Nematode-transmitted plant viruses (such as nepoviruses) cause great economically losses in commercially important plants such as tomatoes, grapevines and raspberries all over the world. To avoid spread of the viruses the interest in mapping the viruses has increased. One of the important nepoviruses infecting European red raspberries (Rubus idaeus) is Tomato black ring virus (TBRV). TBRV has earlier been confirmed in raspberry samples from Belarus by ELISA and the aim of this bachelor degree project was to confirm these results by amplifying, cloning and sequencing the coat protein (CP) gene of the virus. In total eight viral cDNA samples, from two different raspberry samples, were amplified and sequenced. Unfortunately, no sequence matched TBRV, and all analyzed sequences showed a high identity to plant genes and are probably from raspberry. The reason why the amplification failed several times could be because the TBRV strain from Belarus differs from previously known TBRV isolates.

We have obtained precatalytic (enzyme-substrate complex) and postcatalytic (enzyme-product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.

We have obtained precatalytic (enzyme-substrate complex) and postcatalytic (enzyme-product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.