Characterization Of Potato Virus Research Articles

Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses.

Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore’s MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.

Characterization of potato virus Y populations in potato in Israel.

Potato virus Y (PVY) is the most common virus infecting potato worldwide. We analysed potato tuber PVY infections from the major Israeli growing region in 2014-2017. Isolates were characterized by multiplex PCR according to Chikh-Ali et al. (Plant Disease97, 1370, 2013), whose primers were not fully compatible with the Israeli isolates. New primers were designed for a multiplex PCR assay to differentiate the Israeli isolates. Three recombinant strains were observed: PVYNTNa (72% of the isolates), PVYNWi (24%) and PVYSyr-III (found only in 2015). The archetypal PVYO strain was found only once. The classical PVY strains have recently been displaced by recombinant forms, with PVYNTNa dominating. The Israeli isolates appear very similar to those of Europe (the seed tuber source), except for PVYSyr-III.

Incidence and characterization of Potato virus V infections in Iran.

A survey was carried out to determine the extent of Potato virus V (PVV) infection, together with other potyviruses, in Iran in both commercial and local potato varieties. We found a low incidence of PVV in commercial varieties compared to a local potato cultivar Zardi, in which we noted a PVV infection up to ~32.9%. We determined the genomic sequence 9,812 nucleotides of one isolate (KER.LAL.P) from cultivar Agria and the 3'-terminal sequence including coat protein (CP) gene of four additional isolates from cultivar Zardi. The Iranian isolate PVV KER.LAL.P was found to share 91% sequence identity with the Scottish isolate DV-42 (AJ243766) of PVV. The CP gene sequences of the PVV isolates from Iran shared 96.5 to 99.3% pairwise nucleotide identity and they shared <97.5% pairwise identity with the CP sequences of all other PVV isolates available in public databases. Our host studies indicated that the Iranian PVV isolate had a narrower host range and infected Nicotiana debneyi and N. glutinosa test plants. Within the commercial varieties of potato in Iran, we noted a significant amount of mixed potyvirus infection. This study is the first report of occurrence and complete genome of PVV in Iran.

Erratum to: Incidence and Characterization of Potato Virus Y in Seed Potatoes in Tunisia

Erratum to: Potato ResearchDOI 10.1007/s11540-010-9159-9In the original version of this article (Potato Research 53 (3): 151–166) the names oftwo contributing authors were not included. The full list of authors should read:Boukhris-Bouhachem S., Rouze-Jouan J., Khamassi N., Djilani-Khouadja F.,Fakhfakh H., Glais L, Tribodet M, Kerlan C.

Incidence and Characterization of Potato virus Y in Seed Potatoes in Tunisia

Surveys during five consecutive years in four main seed potato- growing areas of Tunisia revealed large differences in Potato virus Y (PVY) incidence. Infection rates at harvest ranged from up to 19% in Cap Bon and in Jendouba, to 31% in Kairouan and 48% in Manouba. However, infection rates were very low across the country in 2003 (1-5%), except in Kairouan, and rather low in 2004 (4-10%). Secondary infections in plants growing from imported seed potatoes were assessed to be 1-6% depending on region and year. Serological analysis of a first set of 90 samples collected in 2004-2005 revealed dominance of the PVY N group (90% of the total number of PVY positives). A second set of 44 isolates from samples collected in 2006 was further analyzed with a combination of serotyping, indexing on tobacco, and RT-PCR tests targeting four genomic regions (5' Ntr/P1, HcPro/P3, CI/NIa, CP). Thirty-five of these 44 isolates were typical PVY NTN isolates, with three recombination junctions in HcPro/P3, CI/NIa, and CP regions, respectively, whereas no recombination junction was identified in the genome of five isolates belonging to the PVY N group. One additional recombinant PVY NTN isolate was recovered from a mixed infection with a PVY O isolate. Only three PVY O isolates were recovered from the samples analyzed.

Characterization of potato virus Y isolates from tomato crops in northeast Spain

A collection of 39 potato virus Y (PVY) isolates from tomato, originating from several commercial crops grown in north-east Spain, was characterised by biological, serological and molecular assays. In general, no correspondence among the three different assays was observed. The results of biological characterization by inoculation of PVY isolates to Nicotiana spp. and pepper plants did not coincide with the differentiation provided by enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies specific to PVYC, PVYO/C or PVYN strains. In some cases this was a consequence of mixed infection of different PVY strains, which selectively infected the different hosts as demonstrated by the ELISA test. Nevertheless, the majority of PVY isolates collected from the same tomato fields showed a high degree of similarity, which indicated the predominance of one-source of infection for each tomato field. Comparison of isolates based on genetic studies did not correspond well with pathological properties, because amplification by reverse transcriptase polymerase chain reaction (RT-PCR) was also selective for some PVY isolates. The sequence analysis of some PVY isolates revealed three main clusters corresponding to NTN and N potato-type strain and NP (non potato-type) strains. Tomato seems to be slightly selective with respect to PVY infection and it is possible to find a great genetic diversity of PVY isolates belonging to different groups, mixtures and probably recombinants, which can complicate the adoption of cultural measures and the development of resistance programmes to control the disease.

Characterization of Potato virus Y (PVY) molecular determinants involved in the vein necrosis symptom induced by PVYN isolates in infected Nicotiana tabacum cv. Xanthi

Viral molecular determinant(s) involved in the tobacco vein necrosis (TVN) symptom induced by necrotic isolates of Potato virus Y (PVY) on Nicotiana tabacum cv. Xanthi leaves remain undetermined. Reference isolates belonging to PVY(N) (infectious PVY(N)-605 clone) and PVY(O) (PVY(O)-139) were used to produce PVY chimeric genomes by using reverse-genetic techniques. These chimeric clones were inoculated biolistically onto Nicotiana clevelandii plants to establish the clone, prior to being tested on N. tabacum for their ability to induce TVN symptoms. Comparison between sequence data and symptoms observed for each mutated PVY construct shows that the C-terminal part of the multifunctional HC-Pro protein includes two residues (K(400) and E(419)) that are involved in TVN induced by PVY(N) isolates. Site-directed mutagenesis was used to confirm that these two HC-Pro residues are involved in the TVN phenotype.

Characterization of Potato Virus M epitopes with the use of synthetic peptides

Characterization of Potato Virus M epitopes with the use of synthetic peptides

Characterization of Potato Virus Y Resistance from Gametoclonal Variation in Flue-Cured Tobacco

A previously identified gametoclonal tobacco variant, NC 602, exhibits resistance to certain potato virus Y (PVY) strains. NC 602 was subjected to a second cycle of anther culture and colchicine treatment. The resulting doubled haploid lines were evaluated for back mutation to susceptibility and any additional mutation that might provide resistance to tobacco etch virus (TEV). The PVY resistance was stable in anther culture, and although no TEV resistance was found, three lines were identified with delayed symptom onset (...)

Characterization of Potato Virus Y Strains Isolated from Pepper

Characterization of Potato Virus Y Strains Isolated from Pepper