First Report of Grapevine yellow speckle viroid-1 and Hop stunt viroid Infecting Grapevines (Vitis vinifera) in India

First report of Grapevine yellow speckle viroid 1 infecting grapevine (Vitis vinifera L.) in Canada

Quebec is the third largest wine grape producer in Canada in acreage, tonnage, and wine grape sales (Carisse et al. 2017; Ben Moussa et al. 2019). To evaluate the diversity of viruses infecting grapevine in Quebec, a total of 77 leaf tissue samples (cv. Vidal) were collected from July to October in 2020 in three different vineyards located in Frelighsburg, Hemmingford and Saint-Jacques-le-Mineur in Quebec, Canada. Double-stranded RNA was extracted from each sample and used for cDNA library preparation with the Nextera XT DNA Library Preparation Kit (Illumina) as described previously (Kesanakurti et al. 2016). High-throughput sequencing (HTS, 2x300 bp) was conducted on dual-indexed libraries in a v3 flow cell using the Illumina MiSeq platform (Adkar-Purushothama et al. 2020). The obtained raw FASTQ data was de-multiplexed into 154 separate sequence files, and the adapters and barcode sequences were trimmed. The quality of the sequences was verified using Trimmomatic V.0.32 and the "clean" sequences were analyzed using Virtool and VirFind virus detection pipelines described elsewhere (Ho and Tzanetakis 2014; Rott et al. 2017) to screen for all possible viruses in the databases. Over 100,000 reads per sample were obtained with a percentage of mapped viral reads ranging from 1.47 to 19.43% of total number of reads. Out of 77 samples, 16 revealed the sequence of grapevine yellow speckle viroid 1 (GYSVd-1), for which the length coverage ranged from 98.5 to 99.1%; the depth ranged from 2X to 856X. The GYSVd-1 positive sequence files were subjected to whole genome assembly on CLC genomics Workbench v20.0.4 with the isolate SY-BR from Brazil (KU880715) used as reference. Seven complete genomes of GYSVd-1 of 366-368 nucleotides (nt) in size were deposited (GenBank Acc. MW732682 to MW732688). BLASTN analysis of the sequences showed 98-100% nt identities with isolate SY-BR. Other viruses and viroids such as Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine rupestris vein feathering virus and Hop stunt viroid were also detected. To confirm GYSVd-1 presence in Quebec vineyards, seven of the 16 HTS-positive grapevine leaf tissue samples were subjected to total RNA extraction, followed by RT-PCR assay as before (Adkar-Purushothama et al. 2015; Sahana et al. 2013); all were positive by RT-PCR. The PCR products were directly Sanger-sequenced, and they showed 100% nt identity to the HTS derived sequences. Three of the seven GYSVd-1 positive grapevines exhibited yellow leaf spots and flecks and tiny yellow leaves, but their mixed infection status makes definitive symptoms association difficult to determine. Previously, Hop stunt viroid was reported from grapevines in Canada (Xiao et al. 2019; Fall et al. 2020) but to the best of our knowledge, this is the first report of GYSVd-1 infecting grapevines in Canada, specifically in the province of Quebec. Further research is required to assess the GYSVd-1 related yield loss. Monitoring and testing for GYSVd-1 infection is necessary to prevent propagation of infected materials, spread, and potential negative impact for the Canadian grapevine industry.

An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids

Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.

Robust Virome Profiling and Whole Genome Reconstruction of Viruses and Viroids Enabled by Use of Available mRNA and sRNA-Seq Datasets in Grapevine (Vitis vinifera L.)

Next-generation sequencing (NGS) based virome analyses of mRNA and sRNA have recently become a routine approach for reliable detection of plant viruses and viroids. In the present study we identified the viral/viroidal spectrum of several Indian grapevine cultivars and reconstructed their whole genomes using the publically available mRNAome and sRNAome datasets. Twenty three viruses and viroids (including two variants of grapevine leafroll associated virus 4) were identified from two tissues (fruit peels and young leaves) of three cultivars among which nine unique grapevine viruses and viroids were identified for the first time in India. Irrespective of the assemblers and tissues used, the mRNA based approach identified more acellular pathogens than the sRNA based approach across cultivars. Further, the mRNAome was on par with the whole transcriptome in viral identification. Through de novo assembly of transcriptomes followed by mapping against reference genome, we reconstructed 19 complete/near complete genomes of identified viruses and viroids. The reconstructed viral genomes included four larger RNA genomes (>13 kb), a DNA genome (RG grapevine geminivirus A), a divergent genome (RG grapevine virus B) and a genome for which no reference is available (RG grapevine virus L). A large number of SNPs detected in this study ascertained the quasispecies nature of viruses. Detection of three recombination events and phylogenetic analyses using reconstructed genomes suggested the possible introduction of viruses and viroids into India from several continents through the planting material. The whole genome sequences generated in this study can serve as a resource for reliable indexing of grapevine viruses and viroids in quarantine stations and certification programs.

Current overview on viroid-host interactions

Viroids are one of the most enigmatic highly structured, circular, single-stranded RNA phytopathogens. Although they are not known to code for any peptide, viroids induce visible symptoms in susceptible host plants that resemble those associated with many plant viruses. It is known that viroids induce disease symptoms by direct interaction with host factors; however, the precise mechanism by which this occurs remains poorly understood. Studies on the host's responses to viroid infection, host susceptibility and nonhost resistance have been underway for several years, but much remains to be done in order to fully understand the complex nature of viroid-host interactions. Recent progress using molecular biology techniques combined with computational algorithms, in particular evidence of the role of viroid-derived small RNAs in the RNA silencing pathways of a disease network, has widened the knowledge of viroid pathogenicity. The complexity of viroid-host interactions has been revealed in the past decades to include, but not be limited to, the involvement of host factors, viroid structural complexity, and viroid-induced ribosomal stress, which is further boosted by the discovery of long noncoding RNAs (lncRNAs). In this review, the current understanding of the viroid-host interaction has been summarized with the goal of simplifying the complexity of viroid biology for future research. This article is categorized under: RNA in Disease and Development > RNA in Disease.

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic)

Comprehensive next generation sequencing virus detection was used to detect the whole spectrum of viruses and viroids in selected grapevines from the Czech Republic. The novel NGS approach was based on sequencing libraries of small RNA isolated from grapevine vascular tissues. Eight previously partially-characterized grapevines of diverse varieties were selected and subjected to analysis: Chardonnay, Laurot, Guzal Kara, and rootstock Kober 125AA from the Moravia wine-producing region; plus Müller-Thurgau and Pinot Noir from the Bohemia wine-producing region, both in the Czech Republic. Using next generation sequencing of small RNA, the presence of 8 viruses and 2 viroids were detected in a set of eight grapevines; therefore, confirming the high effectiveness of the technique in plant virology and producing results supporting previous data on multiple infected grapevines in Czech vineyards. Among the pathogens detected, the Grapevine rupestris vein feathering virus and Grapevine yellow speckle viroid 1 were recorded in the Czech Republic for the first time.

Complete Genome Sequences of Grapevine Yellow Speckle Viroid 1 and Hop Stunt Viroid Assembled from the Transcriptome of Ixeridium dentatum Plants

Here, we report complete genome sequences of grapevine yellow speckle viroid 1 (GYSVd1) and hop stunt viroid (HSVd), members of the family Pospiviroidae, assembled from the transcriptome data generated from Ixeridium dentatum plants. To our knowledge, this is the first report of GYSVd1 and HSVd in I. dentatum.

Detection, distribution, and genetic diversity of Australian grapevine viroid in grapevines in India

Australian grapevine viroid (AGVd) is a viroid specific to grapevine with the least records in the world till date. Here, we report for the first time the presence of AGVd in grapevines in Indian sub-continent. The overall infection rate of AGVd in major grapevine producing areas in India was 9.3 %, which is conspicuously higher than the other regions of the world except for Tunisia and Iran. To understand the AGVd diversity in India, the genetic divergence was examined based on the disparity in the cultivars and the locations. Nucleotide sequence analysis revealed the existence of five major AGVd variants in India besides other 44 minor variants implying the "quasi-species" nature. Further, sequence alignment of all the Indian AGVd variants along with Australian type species underscored the presence of eleven mutation points which are archetypal for Indian AGVd, irrespective of the region, and cultivar of grapevines. Plotting of Indian AGVd sequence variants against Australian type species unveiled that all these eleven mutations are distributed on upper and lower left terminal and pathogenicity regions of the molecule. Phylogenetic analysis divulged all the major Indian AGVd variants formed two distinct clusters, suggesting the two separate evolutionary lineages of AGVd in Indian viticulture.