Production of Double-Stranded RNA in Planta by a Potato Mop-Top Virus (PMTV)-Based Vector for Inducing Gene Silencing

RNA silencing (also known as gene silencing) is an evolutionary conserved mechanism that is involved in regulating gene expression, suppressing mobile elements, and defensing virus infection. RNA silencing is triggered by double-stranded RNA via Dicer or Dicer-like riboendonucleases. DsRNAs are also the replication intermediates of all RNA viruses; as a result, plant RNA viruses are ideal candidates to induce RNA silencing. A large body of plant viruses have been modified into vectors for RNA silencing in varied plant species. Here, we described a simple, time-saving, and operable system for gene function and genetic breeding study of potato and Nicotiana benthamiana using a potato mop-top (MPTV)-based vector.

Evolutionary features of 8K (KDa) silencing suppressor protein of Potato mop-top virus

The cysteine-rich 8K protein of Potato mop-top virus (PMTV) suppresses host RNA silencing. In this study, evolutionary analysis of 8K sequences of PMTV isolates was studied on the basis of nucleotide and amino acid sequences. Twenty-one positively selected sites were identified in 8K coding regions. Recombination events were found in the 8K of PMTV isolates with a rate of 1.8. Totally 30 haplotypes were detected with haplotype diversity ranging from 0.8 to 1.0 and nucleotide diversity from 7.58 to 13.62. The positions 33 and 30 indicated the highly positive and negative selection (with the highest and the lowest dN-dS values), respectively. Tajima's D test suggested that 8K is evolving with a strong positive selection for worldwide isolates. High frequency of segregating sites was identified along 204 positions of 8K. Moreover, in this study, we used Shannon entropy-based approach to evaluate the variability of each site of nucleotide and corresponding amino acid. Based on Shannon entropy method, 139 and 97 nucleotide sites had the highest entropy value, while 47 and 33 amino acid sites showed the most diversity along 8K sequences. Our findings suggest that 8K as an RNA silencing suppressor evolves rapidly. Taken together, its variability might play a big threat to infect other plants or overcome resistant cultivars.

Molecular and pathobiological characterization of 61 Potato mop-top virus full-length cDNAs reveals great variability of the virus in the centre of potato domestication, novel genotypes and evidence for recombination

The evolutionary divergence of Potato mop-top virus (PMTV), a tri-partite, single-stranded RNA virus, is exceptionally low, based on the analysis of sequences obtained from isolates from Europe, Asia and North America. In general, RNA viruses exist as dynamic populations of closely related and recombinant genomes that are subjected to continuous genetic variation. The reason behind the low genetic variation of PMTV remains unclear. The question remains as to whether the low variability is a shared property of all PMTV isolates or is a result of the limited number of isolates characterized so far. We hypothesized that higher divergence of the virus might exist in the Andean regions of South America, the centre of potato domestication. Here, we report high variability of PMTV isolates collected from 12 fields in three locations in the Andean region of Peru. To evaluate PMTV genetic variation in Peru, we generated full-length cDNA clones, which allowed reliable comparative molecular and pathobiological characterization of individual isolates. We found significant divergence of the CP-RT and 8K sequences. The 8K cistron, which encodes a viral suppressor of RNA silencing, was found to be under diversifying selection. Phylogenetic analysis determined that, based on the CP-RT sequence, all PMTV isolates could be categorized into three separate lineages (clades). Moreover, we found evidence for recombination between two clades. Using infectious cDNA clones of the representatives of these two clades, as well as reassortants for the RNA-CP genomic component, we determined the pathobiological differences between the lineages, which we coined as S (for severe) and M (for mild) types. Interestingly, all isolates characterized previously (from Europe, Asia and North America) fall into the S-type clade, whereas most of the Peruvian isolates belong to the M-type. Taken together, our results support the notion of the single introduction of PMTV from the centre of potato origin to Europe, and subsequent spread of the S-type into Asia and USA. This is also supported by the suggested novel classification of isolates based on genetic constellations.

Development and Optimization of a Reverse Transcription Hemi-Nested PCR Primer for the Detection of Potato Mop-Top Virus at Quarantine Inspection Sites in Korea

Potato mop-top virus (PMTV) is classified as a plant quarantine virus in Korea. It is tested at import inspection sites. In this study, two sets of reverse transcription-hemi-nested polymerase chain reaction primers were developed to diagnose PMTV. In addition, modified- positive control plasmid was developed for the identification of false positive results in plant quarantine. The assay is expected to be useful for improving the detection and diagnosis of PMTV.