Not Available

Not AvailableBackground Tomato spotted wilt virus (TSWV; Tospovirus: Bunyaviridae) has been an economically important virus in the USA for over 30 years. However the complete sequence of only one TSWV isolate PA01 characterized from pepper in Pennsylvania is available. Results The large (L) RNA of a TSWV WA-USA isolate was cloned and sequenced. It consisted of 8914 nucleotides (nt) encoding a single open reading frame of 8640 nts in the viral-complementary sense. The ORF potentially codes for RNA-dependent RNA polymerase (RdRp) of 330.9 kDa. Two untranslated regions of 241 and 33 nucleotides were present at the 5′ and 3′ termini, respectively that shared conserved tospoviral sequences. Phylogenetic analysis using nucleotide sequences of the complete L RNA showed that TSWV WA-USA isolate clustered with the American and Asian TSWV isolates which formed a distinct clade from Euro-Asiatic Tospoviruses. Phylogeny of the amino acid sequence of all tospoviral RdRps used in this study showed that all the known TSWV isolates including the USA isolate described in this study formed a distinct and a close cluster with that of Impateins necrotic spot virus. Multiple sequence alignment revealed conserved motifs in the RdRp of TSWV. Recombination analysis identified two recombinants including the TSWV WA-USA isolate. Among them, three recombination events were detected in the conserved motifs of the RdRp. Conclusions Sequence analysis and phylogenetic analysis of the L RNA showed distinct clustering with selected TSWV isolates reported from elsewhere. Conserved motifs in the core polymerase region of the RdRp and recombination events were identifiedDBT CREST AWAR

Not Available

Annual meeting of the American Phytopathological Society, Minneapolis Convention Center, Minneapolis, MN, August 9-13, 2014Small non-coding RNAs are important effector molecules in response to pathogen invasion in plants and animals. We conducted in silico analysis of the DNA genomes of two distinct species of genus Begomovirus (family Geminiviridae)-Mungbean yellow mosaic India virus (MYMIV) and Mungbean yellow mosaic virus (MYMV)-that infect soybean using a micro-RNA (miRNA) target prediction algorithm, plant small RNA target analysis server. MYMV displays greater vulnerability to plant miRNAs with 99 miRNAs targeting its genome, whereas 70 miRNAs appear to be targeting the MYMIV genome. miRNAs derived from Glycine max, Glycine soja and Cajanus cajan display 63, 18, and 8 potential target sites on the begomovirus genomes. Among the non-host plants, begomoviruses exhibit seven and six potential target sites for O. sativa, and P. trichocarpa-derived miRNAs respectivelyNot Availabl

Not Available

Not AvailableTomato spotted wilt virus (TSWV; Tospovirus:Bunyaviridae) is one of the most prolific and economically important viruses of field and horticultural crops. In the plant-virus interactions, virus-derived siRNAs (vsiRNAs) are the result of activity of host-mediated silencing mechanism. We recently obtained the TSWV-specific small RNA profiles from virus-infected tomato. A subset of siRNAs derived from the TSWV genome hotspots was analyzed in silico for their propensity to down regulate tomato transcriptome. vsiRNAs were found to interact with a gamut of host genes involved in basal cellular activities such as nucleic acid metabolism, ribosomal turnover, translational factors, cytoskeletal proteins, phenylpropanoid biosynthesis, glycosyl transferases, peptidases, hormonal signalling, protein kinases, intercellular transporter genes, and stress-related proteins. Notably, vsiRNAs derived from the TSWV NSs gene binds with transcripts generally associated with stress signalling, whereas siRNAs from NSm were predominantly found to bind the transcripts involved in abiotic stress responses such as dehydration responsive protein, ion exchange transporters, and low temperature and salt responsive proteins. The predicted interactome scenario when validated through gene expression studies using RNAseq could provide a detailed picture on the molecular mechanism underlying the tospovirus-plant interactions.Not Availabl

Not Available

Not AvailablePotato mop-top virus (PMTV) is the type species of genus Pomovirus, family Virgaviridae. The occurrence of PMTV was reported recently in the Pacific Northwestern USA. PMTV genome is characterized by three linear positive sense ssRNA molecules. As part of a study to better understand the virus biology and molecular biology, the genome of a WA isolate was characterized and we report the complete nucleotide (nt) sequence of the genomic components RNA-2, and RNA-3. RNA2 was 3134nt in length with an ORF between nt positions 314-844 that codes for the coat protein and the same ORF as a read-through extends further to nt position 2791 coding for the CPread through protein. RNA 3 was 2964nt in length and potentially encodes four ORFs – three of them forming the triple gene bock (TGB) that was shown to be involved in cell to cell movement. RNA2 also contains a 206 nt ORF present toward the 3’ end that encodes a cysteine-rich 8K protein. RFLP analysis of RNA2 and RNA 3 of the WA isolate revealed the combination of RNA2-II and RNA3-B types, the combination that is prevalent in Europe and elsewhere. The sequenced regions had 99% sequence identity with the corresponding RNA components reported from Europe. The high degree of sequence identity could be useful in developing virus detection tools and for designing RNAi-based virus management strategies.Not Availabl

Not Available

Not AvailableThrips-transmitted Iris yellow spot virus is an economically important viral pathogen of Allium crops worldwide. A global genetic analysis of known IYSV nucleocapsid gene (N gene) sequences was carried out to determine the comparative population structure, spatial and temporal dynamics with reference to its genetic diversity and evolution. A total of 98 complete N gene equences available in GenBank and reported from 23 countries were characterized by in silico RFLP analysis. Based on RFLP, 94% of the isolates could be grouped into NL or BR types while the rest belonged to neither group. The relative proportion of NL and BR types was 46% and 48%, respectively. A temporal shift in the IYSV genotypes with a greater incremental incidence of IYSVBR was found over IYSVNL before 2005 compared to after 2005. The virus population had at least one evolutionarily significant recombination event, involving IYSVBR and IYSVNL. Genetic differentiation studies showed inherent differentiation and infrequent gene flow between IYSVBR and IYSVNL genotypes corroborating the geographical confinement of these genotypes. Taken together the study suggests that the observed diversity in IYSV population and temporal shift in IYSVBR genotype is attributable to genetic recombination, abundance of purifying selection, insignificant positive selection and population expansionNot Availabl