Black currant reversion virus, a mite-transmitted nepovirus

Viral diseases of fruit and berry crops in the South of the Russian Far East

Aim. To systematise data on pathogens of viral diseases of garden and berry crops in the south of the Russian Far East.

Discussion. The peculiar climatic features of the Far East limit the range of garden and berry crops. However, there are a significant number of species of wild fruits and berry plants in the region, which have increased (often – record breaking) frost resistance and are therefore actively used for breeding new cultural forms. At the same time, for the last century and a half new varieties of garden crops have been actively introduced to the Far East, which has lead to an increase in the risk of penetration of entire phytovirus complexes together with vegetatively propagated (cuttings, vaccinations) plants. The greatest damage to garden crops in the Far East is caused by a number of representatives of the genus Nepovirus (Picornavirales: Secoviridae): Tomato ringspot virus, Arabis mosaic virus, Raspberry ringspot virus, Grapevine fanleaf virus, Grapevine linear pattern virus as well as several still unidentified viruses. Among other taxonomic groups of phytoviruses dangerous for fruit and berry crops one could point out Potato virus Y (Patatavirales: Potyviridae, Potyvirus), Carnation ringspot virus (Tolivirales: Tombusviridae, Dianthovirus), Clover yellow mosaic virus (Tymovirales: Alphaflexiviridae, Potexvirus), Cucumber mosaic virus (Martellivirales: Bromoviridae, Cucumovirus), Alfalfa mosaic virus (Martellivirales: Bromoviridae, Alfamovirus). The paper considers the species composition of aphids‐carriers of phytoviruses affecting garden crops of the region.

Conclusions. In connection with the further prospects for the development of horticulture in the Russian Far East, it is necessary to intensify ecological and virological studies of this section of phytovirology as well as to increase access to agricultural producers with available test systems.

Analysis of R Genes Related to Blackcurrant Reversion Virus Resistance in the Comparative Transcriptome of Ribes nigrum cv. Aldoniai

Blackcurrant reversion virus (BRV) is the most destructive mite-transmitted pathogen in blackcurrants. The understanding of the resistance to BRV is limited, hindering and delaying the selection process. To identify the resistance (R) gene for BRV resistance, a gene expression analysis based on de novo blackcurrant cv. Aldoniai comparative transcriptome analysis (mock- and BRV-inoculated samples at 2 and 4 days post-inoculation (dpi)) was performed. In this study, 111 annotated clusters associated with pathogenesis according to conservative R gene domains were identified. In virus-infected samples, only Cluster-12591.33361 showed significant expression at 4 dpi. The expression profiles of this cluster were significantly associated with the presence of BRV particles in plant tissues, making it a putative R gene in the dominant resistance strategy in the BRV-Ribes nigrum interaction. The newly identified gene R.nigrum_R belongs to the CC-NBS-LRR class and has 63.9% identity with RPM1 in Populus spp. This study provides new insights on dominant putative R genes related to resistance to BRV in R. nigrum, which could aid targeted research and genetic improvement in breeding programs of blackcurrants.

De Novo Transcriptome Analysis of R. nigrum cv. Aldoniai in Response to Blackcurrant Reversion Virus Infection

The most damaging pathogen in blackcurrant plantations is mite-transmitted blackcurrant reversion virus (BRV). Some Ribes species have an encoded genetic resistance to BRV. We performed RNA sequencing analysis of BRV-resistant blackcurrant cv. Aldoniai to evaluate the molecular mechanisms related to the BRV infection response. The RNA of virus-inoculated and mock-inoculated microshoots was sequenced, and the transcriptional changes at 2- and 4-days post inoculation (dpi) were analyzed. The accumulation and expression of BRV RNA1 were detected in infected plants. In total, 159,701 transcripts were obtained and 30.7% were unigenes, annotated in 7 databases. More than 25,000 differentially expressed genes (DEGs) according to FPKM were upregulated or downregulated. We observed 221 and 850 DEGs at 2 and 4 dpi, respectively, in BRV-infected microshoots related to the stress response. The proportion of upregulated DEGs at 4 dpi was about 3.5 times higher than at 2 dpi. Pathways of the virus defense response were activated, and key candidate genes were identified. The phenylpropanoid and the cutin, suberine, and wax biosynthesis pathways were activated in infected plants. Our comparative de novo analysis of the R. nigrum transcriptome provides clues not only for understanding the molecular BRV resistance mechanisms but also for breeding BRV-tolerant genotypes.

An Effective Method of Ribes spp. Inoculation with Blackcurrant Reversion Virus under In Vitro Conditions

Blackcurrant reversion virus (BRV) is the most destructive currant-infecting and mite-transmitted pathogen from the genus Nepovirus. In this work, BRV transmission in the system Ribes ex vitro-Ribes in vitro was applied for the first time. Triple infection of BRV identified in blackcurrant cv. Gojai was used for phylogenetic analysis and inoculation assay. Transmission of BRV was successful due to its stability in the inoculum for up to 8 days at 4 °C; all BRV isolates were infectious. Our suggested inoculation method through roots was applied in six Ribes spp. genotypes with 100.0% reliability, and the expression levels of defence-related gene PR1 to biotic stress was observed. The prevalence of the virus in microshoots after 2-14 days post-inoculation (dpi) was established by PCR. In resistant genotypes, the BRV was identified up to 8 dpi; meanwhile, infection remained constant in susceptible genotypes. We established that BRV transmission under controlled conditions depends on the inoculum quality, post-inoculation cultivation temperature, and host-plant susceptibility to pathogen. This in vitro inoculation method opens possibilities to reveal the resistance mechanisms or response pathways to BRV and can be used for the selection of resistant Ribes spp. in breeding programs.

Characterization of a New Nepovirus Infecting Grapevine

In 2012, dormant canes of a proprietary wine grape (Vitis vinifera L.) accession were included in the collection of the University of California-Davis Foundation Plant Services. No virus-like symptoms were elicited when bud chips from propagated own-rooted canes of the accession were graft-inoculated onto a panel of biological indicators. However, chlorotic ringspot symptoms were observed on sap-inoculated Chenopodium amaranticolor Coste & A. Rein and C. quinoa Willd. plants, indicating the presence of a mechanically transmissible virus. Transmission electron microscopy of virus preparations from symptomatic C. quinoa revealed spherical, nonenveloped virions about 27 nm in diameter. Nepovirus-like haplotypes of sequence contigs were detected in both the source grape accession and symptomatic C. quinoa plants via high-throughput sequencing. A novel bipartite nepovirus-like genome was assembled from these contigs, and the termini of each RNA segment were verified by rapid amplification of complementary DNA ends assays. The RNA1 (7,186-nt) of the virus encodes a large polyprotein 1 of 231.1 kDa, and the RNA2 (4,460-nt) encodes a large polyprotein 2 of 148.9 kDa. Each of the polyadenylated RNA segments is flanked by 5'- (RNA1 = 156-nt; RNA2 = 170-nt) and 3'- (RNA1 = 834-nt; RNA2 = 261-nt) untranslated region sequences with >90% identities. Maximum likelihood phylogenetic analyses of the conserved Pro-Pol amino acid sequences revealed the clustering of the new virus within the genus Nepovirus of the family Secoviridae. Considering its biological and molecular characteristics, and based on current taxonomic criteria, we propose that the novel virus, named grapevine nepovirus A, be assigned to the genus Nepovirus.

Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium

High throughput sequencing was performed on virion-associated nucleic acids (VANA) from a pool of fifty asymptomatic rough bluegrasses (Poa trivialis L.) collected in a Belgian grazed pasture. Bioinformatics analyses produced some contigs presenting similarities with secovirid genomes, in particular nepoviruses and waikaviruses. Three distinct positive-sense single-stranded RNAs including 5' and 3' UTR were reconstructed and they represented two novel viruses infecting rough bluegrass, for which the provisional names poaceae Liege nepovirus A (PoLNVA, 7298 nt for RNA1 and 4263 nt for RNA2) and poaceae Liege virus 1 (PoLV1, 11,623 nt) were proposed. Compared to other Secoviridae members, the highest amino acid identity reached 90.7 % and 66.7 % between PoLNVA and nepoviruses for the Pro-Pol and CP regions respectively, while PoLV1 presented the highest amino acid identity with waikaviruses but with lower identities, i.e. 41.2 % for Pro-Pol and 25.8 % for CP regions, far below the ICTV demarcation criteria for novel secovirid. Based on sequence identity and phylogenetic analyses, PoLNVA was proposed to belong to the genus Nepovirus and PoLV1 as an unclassified secovirids. Detection of the two novel viruses was confirmed in high prevalence in rough bluegrass and ten other wild Poaceae species (Agropyron repens, Agrostis capillaris, Apera spica-venti, Anthoxanthum odoratum, Cynosorus cristatus, Festuca rubra, Holcus lanatus, Lolium perenne, Phleum bertolini and Phleum pratense) by RT-PCR and Sanger sequencing, revealing a diverse host range within Poaceae for these novel secovirids. Seed transmission was evaluated and confirmed for PoLNVA.

Small-RNA analysis of pre-basic mother plants and conserved accessions of plant genetic resources for the presence of viruses

Pathogen-free stocks of vegetatively propagated plants are crucial in certified plant production. They require regular monitoring of the plant germplasm for pathogens, especially of the stocks maintained in the field. Here we tested pre-basic mother plants of Fragaria, Rubus and Ribes spp., and conserved accessions of the plant genetic resources of Rubus spp. maintained at research stations in Finland, for the presence of viruses using small interfering RNA (siRNA) -based diagnostics (VirusDetect). The advance of the method is that unrelated viruses can be detected simultaneously without resumptions of the viruses present. While no virus was detected in pre-basic mother plants of Fragaria and Ribes species, rubus yellow net virus (RYNV) was detected in pre-basic mother plants of Rubus. Raspberry bushy dwarf virus (RBDV), black raspberry necrosis virus (BRNV), raspberry vein chlorosis virus (RVCV) and RYNV were detected in the Rubus genetic resource collection. The L polymerase encoding sequence characterized from seven RVCV isolates showed considerable genetic variation. The data provide the first molecular biological evidence for the presence of RYNV in Finland. RYNV was not revealed in virus indexing by indicator plants, which suggests that it may be endogenously present in some raspberry cultivars. In addition, a putative new RYNV-like badnavirus was detected in Rubus spp. Blackcurrant reversion virus (BRV) and gooseberry vein banding associated virus (GVBaV) were detected in symptomatic Ribes plants grown in the field. Results were consistent with those obtained using PCR or reverse transcription PCR and suggest that the current virus indexing methods of pre-basic mother plants work as expected. Furthermore, many new viruses were identified in the collections of plant genetic resources not previously tested for viruses. In the future, siRNA-based diagnostics could be a useful supplement for the currently used virus detection methods in certified plant production and thus rationalize and simplify the current testing system.

Genome sequence and detection of peach rosette mosaic virus

Peach rosette mosaic disease was first described in the 1940s affecting peach and plum. It was later determined that peach rosette mosaic virus (PRMV) is the causal agent of the disease. PRMV, a member of the genus Nepovirus, infects several perennial crops including stone fruit, grape and blueberry as well as several weed species found in orchards around the world. The molecular characterization of the virus is limited to partial genome sequences making it difficult to develop reliable and sensitive molecular detection tests; the reason that detection is routinely performed using ELISA with antibodies risen against a single virus isolate. Given the potential economic impact of the virus and the modes of transmission which, in addition to nematodes, include seed we studied PRMV in more depth using a modified dsRNA extraction protocol to obtain the virus genome. We determined the full nucleotide sequence and developed a protocol that detects conserved regions present in RNA 1 and RNA 2, making it an excellent alternative to the detection protocols used today.

Molecular characterization of a new soybean-infecting member of the genus Nepovirus identified by high-throughput sequencing

The complete nucleotide sequence of a new soybean-infecting member of the genus Nepovirus (provisionally named "soybean latent spherical virus" [SLSV]) was identified by high-throughput sequencing of RNAs from soybean leaf samples from North Dakota, USA. The sequences of RNAs 1 (8,190 nt) and 2 (5,788 nt) were completed by rapid amplification of cDNA ends. Each contained a single long open reading frame and a 3' nontranslated region of greater than 1,500 nt. The predicted amino acid sequences of the two ORFs were most closely related to nepoviruses in subgroup C. Full-length cDNAs of RNAs 1 and 2 were cloned and used to inoculate soybean plants, which did not display obvious symptoms. These results suggest that SLSV represents a new species in the genus Nepovirus.

Control of virus diseases of berry crops

Virus control in berry crops starts with the development of plants free of targeted pathogens, usually viruses, viroids, phytoplasmas, and systemic bacteria, through a combination of testing and therapy. These then become the top-tier plants in certification programs and are the source from which all certified plants are produced, usually after multiple cycles of propagation. In certification schemes, efforts are made to produce plants free of the targeted pathogens to provide plants of high health status to berry growers. This is achieved using a systems approach to manage virus vectors. Once planted in fruit production fields, virus control shifts to disease control where efforts are focused on controlling viruses or virus complexes that result in disease. In fruiting fields, infection with a virus that does not cause disease is of little concern to growers. Virus control is based on the use of resistance and tolerance, vector management, and isolation.

Complete nucleotide sequences and genome organization of a cherry isolate of cherry leaf roll virus

The complete nucleotide sequence of cherry leaf roll virus (CLRV, genus Nepovirus) from a naturally infected cherry tree (Prunus avium cv. Bing) in North America was determined. RNA1 and RNA2 consist of 7,893 and 6,492 nucleotides, respectively, plus a poly-(A) tail. Each RNA encodes a single potential open reading frame. The first 657 nucleotides of RNA1 and RNA2 are 99% identical and include the 5'-UTR and the first 214 deduced amino acids of the polyproteins following the first of two in-frame start codons. Phylogenetic analysis reveals close relationships between CLRV and members of subgroup C of the genus Nepovirus.

What's "cool" on eriophyoid mites?

Fundamental knowledge on the morphology, biology, ecology, and economic importance of Eriophyoidea has been exhaustively compiled by Lindquist et al. (Eriophyoid mites--their biology, natural enemies and control; Elsevier, 1996). Since that time, the number of recognized species and the economic importance of the taxon have increased substantially. The aim of this paper is to analyze and briefly review new findings from eriophyoid mites' literature after Lindquist et al. book, stressing persistent gaps and needs. Much recent attention has been given to sampling and detection, taxonomy and systematics, faunistic surveys, internal morphology, rearing techniques, biological and ecological aspects, biomolecular studies, and virus vectoring. Recommendations are made for integrating research and promoting broader dissemination of data among specialists and non-specialists.

Elucidation of the Roles of Blackcurrant reversion virus and Phytoplasma in the Etiology of Full Blossom Disease in Currants

To determine the roles of phytoplasmas and Blackcurrant reversion virus (BRV) in the etiology of full blossom disease (FBD), we conducted graft and dodder transmission experiments. Scions from FBD-affected Ribes rubrum were grafted onto red currants, white currants, and black currants. Red and white cultivars revealed symptoms of FBD, whereas blackcurrant displayed symptoms of BRV. No differences in symptoms were observed between plants infected with BRV only and those infected with BRV and phytoplasma. Aster yellows phytoplasma subgroup 16SrI-C was transferred from FBD-infected red currants to periwinkle, where symptoms of green and yellow petal were observed. Back-transmission of phytoplasma to currant seedlings of red and black currant was not successful. Scions of periwinkle infected with aster yellows phytoplasmas of subgroup 16SrI-C and 16SrI-B, which were bottle-, bark-, and approach-grafted onto seedlings of red and black currant, resulted in positive but symptomless transmission of phytoplasma to red currant. We conclude that FBD symptoms are induced by BRV rather than by phytoplasma, which was originally described as the causal agent of FBD.

Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology

A novel, unbiased approach to plant viral disease diagnosis has been developed which requires no a priori knowledge of the host or pathogen. Next-generation sequencing coupled with metagenomic analysis was used to produce large quantities of cDNA sequence in a model system of tomato infected with Pepino mosaic virus. The method was then applied to a sample of Gomphrena globosa infected with an unknown pathogen originally isolated from the flowering plant Liatris spicata. This plant was found to contain a new cucumovirus, for which we suggest the name 'Gayfeather mild mottle virus'. In both cases, the full viral genome was sequenced. This method expedites the entire process of novel virus discovery, identification, viral genome sequencing and, subsequently, the development of more routine assays for new viral pathogens.

Translation mechanisms involving long-distance base pairing interactions between the 5' and 3' non-translated regions and internal ribosomal entry are conserved for both genomic RNAs of Blackcurrant reversion nepovirus

One of the mechanisms of functioning for viral cap-independent translational enhancers (CITEs), located in 3' non-translated regions (NTRs), is 3' NTR-5' leader long-distance base pairing. Previously, we have demonstrated that the RNA2 3' NTR of Blackcurrant reversion nepovirus (BRV) contains a CITE, which must base pair with the 5' NTR to facilitate translation. Here we compared translation strategies employed by BRV RNA1 and RNA2, by using mutagenesis of the BRV NTRs in firefly luciferase reporter mRNA, in plant protoplasts. Translation mechanisms, based on 3' CITEs, 5' NTR-3' NTR base pairing and poly(A) tail-stimulation, were found conserved between RNA1 and RNA2. The 40S ribosomal subunit entry at the RNA1 leader occurred, at least partly, via an internal ribosomal entry site (IRES). Two RNA1 leader segments complementary to plant 18S rRNA enhanced translation. A model for BRV RNAs translation, involving IRES-dependent 40S subunit recruitment and long-distance 5' NTR-3' NTR base pairing, is discussed.

The RNA2 5' leader of Blackcurrant reversion virus mediates efficient in vivo translation through an internal ribosomal entry site mechanism

The 5' and 3' non-translated regions (NTRs) of mRNAs of eukaryotes and their viruses often contain translational enhancers, including internal ribosomal entry sites (IRESs) comprised in the 5' leaders of many uncapped viral mRNAs. Blackcurrant reversion virus (BRV) has a genome composed of two uncapped, polyadenylated RNAs with relatively short 5' NTRs, almost devoid of secondary structure. In this work, a role of the RNA2 5' NTR in translation was studied by using mono- and dicistronic Photinus pyralis and Renilla reniformis luciferase reporter mRNAs in protoplasts of Nicotiana benthamiana. The RNA2 5' leader was found to confer efficient in vivo translation compared with the control 5' NTR, and each half of the BRV leader was essential for stimulatory function. Such efficient translational enhancement was mediated, at least in part, through an IRES mechanism. Multiple RNA2 5' NTR regions, complementary to a fragment of plant 18S rRNA demonstrated previously to be accessible for intermolecular mRNA-rRNA interactions and conserved between eukaryotes, were shown to be important for efficient translation. Similar mRNA-rRNA base-pairing potential was also predicted for the 5' leaders of other nepoviruses.

Role of the RNA2 3' non-translated region of Blackcurrant reversion nepovirus in translational regulation

The 3' non-translated regions (NTRs) of mRNAs of eukaryotes and their viruses often contain translational enhancers (TEs). Blackcurrant reversion nepovirus (BRV) has a genome composed of two uncapped polyadenylated RNAs with very long 3' NTRs, nucleotide sequences of which are very conserved between different BRV isolates. In this work, we studied a role of the RNA2 3' NTR in translation, using mutagenesis of the firefly luciferase reporter mRNA, in protoplasts of Nicotiana benthamiana. The RNA2 3' NTR was found to contain a cap-independent TE (3' CITE), which must base pair with the 5' NTR to facilitate translation. The BRV 3' CITE and poly(A) tail provided a major contribution to translational efficiency, with less input from other 3' NTR parts. The BRV 3' CITE does not share similarity in nucleotide sequence and secondary structure with other viruses and thus represents a new class of 3' CITE.