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

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 478 ◽  
Author(s):  
Michele Della Bartola ◽  
Stephen Byrne ◽  
Ewen Mullins
Keyword(s):  
Genetic Diversity ◽  
Potato Virus ◽  
Potato Virus Y ◽  
De Novo ◽  
Solanum Tuberosum L ◽  
Germplasm Collection ◽  
Whole Genome Sequence ◽  
Nanopore Sequencing ◽  
High Genetic Diversity ◽  
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.

scholarly journals Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 753
Author(s):  
Miroslav Glasa ◽  
Richard Hančinský ◽  
Katarína Šoltys ◽  
Lukáš Predajňa ◽  
Jana Tomašechová ◽  
...  
Keyword(s):  
High Throughput ◽  
Potato Virus ◽  
Mixed Infection ◽  
High Throughput Sequencing ◽  
Potato Virus Y ◽  
De Novo ◽  
Sweet Pepper ◽  
Complete Sequence ◽  
Genome Region ◽  
Mapping Parameters

In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection.

Genetic Diversity of Potato Virus Y in Belarus

2021 ◽  
Vol 55 (3) ◽  
pp. 290-297
Author(s):  
P. V. Kuzmitskaya ◽  
T. M. Dzmitrieva ◽  
E. S. Karaleva ◽  
O. Yu. Urbanovich ◽  
V. L. Makhanko ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Potato Virus ◽  
Potato Virus Y

scholarly journals Arbuscular Mycorrhiza Changes the Impact of Potato Virus Y on Growth and Stress Tolerance of Solanum tuberosum L. in vitro

2020 ◽  
Vol 10 ◽  
Author(s):  
Edyta Deja-Sikora ◽  
Anita Kowalczyk ◽  
Alina Trejgell ◽  
Adriana Szmidt-Jaworska ◽  
Christel Baum ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Arbuscular Mycorrhiza ◽  
Stress Tolerance ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Solanum Tuberosum L ◽  
The Impact

scholarly journals Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants

2018 ◽  
Vol 31 (7) ◽  
pp. 707-723 ◽  
Author(s):  
Silvia Turco ◽  
Victor Golyaev ◽  
Jonathan Seguin ◽  
Céline Gilli ◽  
Laurent Farinelli ◽  
...  
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
De Novo ◽  
Cross Protection ◽  
Mixed Infections ◽  
Antiviral Defense ◽  
Viral Quasispecies ◽  
Genome Sequences ◽  
Depth Analysis

In plants, RNA silencing–based antiviral defense generates viral small RNAs (sRNAs) faithfully representing the viral genomes. We employed sRNA sequencing and bioinformatics (sRNA-omics) to characterize antiviral defense and to reconstruct the full genomic sequences and their variants in the evolving viral quasispecies in cultivated solanaceous plants carrying mixed infections. In naturally infected Solanum tuberosum (potato), one case study revealed a virome comprising Potato virus Y (genus Potyvirus) and Potato virus X (genus Potexvirus), which was reconstructed by de novo–assembling separate genome-size sRNA contigs. Another case study revealed a virome comprising NTN and O strains of Potato virus Y, whose sRNAs assembled in chimeric contigs, which could be disentangled on the basis of reference genome sequences. Both viromes were stable in vegetative potato progeny. In a cross-protection trial of Solanum lycopersicum (tomato), the supposedly protective mild strain CH2 of Pepino mosaic virus (genus Potexvirus) was tested for protection against strain LP of the same virus. Reciprocal mechanical inoculations eventually resulted in co-infection of all individual plants with CH2 and LP strains, reconstructed as separate sRNA contigs. LP invasions into CH2-preinfected plants and vice versa were accompanied by alterations of consensus genome sequences in viral quasispecies, indicating a potential risk of cross-protection measures. Additionally, the study also revealed, by reconstruction from sRNAs, the presence of the mechanically nontransmissible Southern tomato virus (genus Amalgavirus) in some plants. Our in-depth analysis of sRNA sizes, 5′-nucleotide frequencies and hotspot maps revealed similarities in sRNA-generating mechanisms in potato and tomato, differential silencing responses to virome components and potential for sRNA-directed cross-targeting between viral strains which could not, however, prevent the formation of stable viromes.

Genetic Diversity of Potato virus Y Complex

2012 ◽  
Vol 90 (1) ◽  
pp. 7-13 ◽  
Author(s):  
Alexander V. Karasev ◽  
Stewart M. Gray
Keyword(s):  
Genetic Diversity ◽  
Potato Virus ◽  
Potato Virus Y

Role of Hairy Nightshade in the Transmission of Different Potato virus Y Strains on Solanum tuberosum (L.)

2010 ◽  
Vol 11 (1) ◽  
pp. 38 ◽  
Author(s):  
Felix A. Cervantes ◽  
Juan M. Alvarez
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
Green Peach Aphid ◽  
Transmission Rate ◽  
Solanum Tuberosum L ◽  
Macrosiphum Euphorbiae ◽  
Invasive Weed ◽  
Potato Plants ◽  
Tuber Necrosis

The complexity of the Potato virus Y (PVY) (Potyviridae: Potyvirus) pathosystem is affected by the presence of several virus strains that differ in their ability to produce tuber necrosis and by the presence of an alternate host that could increase the amount of inoculum in potato fields. Solanum sarrachoides (Sendtner) is an invasive weed from South America present in Pacific Northwest potato agro-ecosystems. It serves as reservoir of PVY and its most efficient vectors: the green peach aphid, Myzus persicae (Sulzer), and the potato aphid, Macrosiphum euphorbiae (Thomas). The role of S. sarracoides as vector and virus reservoir in PVY epidemiology was investigated through a series of laboratory and greenhouse experiments. We studied the symptoms produced in S. sarracoides upon infection with necrotic and non-necrotic strains of PVY and looked at the percentage of infection and titer accumulation of these strains. PVY infection in S. sarrachoides produced symptoms similar to those produced in PVY-infected potato plants. Mottling and yellowing were the main symptoms of infection observed in S. sarrachoides plants, especially by PVYO and PVYNTN infection. Greenhouse transmission studies revealed that PVY-infected S. sarrachoides increased the transmission rate of PVY necrotic strains by M. persicae. The necrotic strain PVYNTN reached higher titer in S. sarrachoides than in potato plants when compared to PVYO and PVYN:O These findings have broadened our understanding of the role and importance of S. sarrachoides in the PVY epidemiology in the potato ecosystems and could potentially be included in the development or optimization of virus management programs. Accepted for publication 15 March 2010. Published 26 May 2010.

Novel somatic hybrids (Solanum tuberosum L. + Solanum tarnii) and their fertile BC1 progenies express extreme resistance to potato virus Y and late blight

2008 ◽  
Vol 116 (5) ◽  
pp. 691-700 ◽  
Author(s):  
Ramona Thieme ◽  
Elena Rakosy-Tican ◽  
Tatjana Gavrilenko ◽  
Olga Antonova ◽  
Jörg Schubert ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Late Blight ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Somatic Hybrids ◽  
Solanum Tuberosum L ◽  
Extreme Resistance

Genetic diversity of potato virus Y (PVY): sequence analyses reveal ten novel PVY recombinant structures

2017 ◽  
Vol 163 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Kelsie J. Green ◽  
Celeste J. Brown ◽  
Alexander V. Karasev
Keyword(s):  
Genetic Diversity ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Sequence Analyses

scholarly journals Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection

Proteomes ◽  
2017 ◽  
Vol 5 (4) ◽  
pp. 14 ◽  
Author(s):  
Tjaša Stare ◽  
Katja Stare ◽  
Wolfram Weckwerth ◽  
Stefanie Wienkoop ◽  
Kristina Gruden
Keyword(s):  
Solanum Tuberosum ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Solanum Tuberosum L ◽  
Transcriptome Response

scholarly journals First Report of Potato virus Y in Potato in Tajikistan

Plant Disease ◽  
2012 ◽  
Vol 96 (7) ◽  
pp. 1074-1074 ◽  
Author(s):  
O. J. Alabi ◽  
J. M. Crosslin ◽  
N. Saidov ◽  
R. A. Naidu
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
Solanum Tuberosum L ◽  
Disease Incidence ◽  
Pairwise Comparison ◽  
Mixed Infections ◽  
Rt Pcr ◽  
Fta Cards ◽  
Tuber Necrosis ◽  
Two Samples

Potato (Solanum tuberosum L.) is widely grown as a staple food and cash crop in Tajikistan and is an important food security crop in the country. In June 2011, we conducted a survey of potatoes in farmers' fields in the Buston and Dushanbe regions (about 200 miles apart) of Tajikistan. Potato plants with stunted growth and leaves showing chlorotic spots, curling, and necrotic spots and rings were observed with the disease incidence monitored in 10 fields each in Buston and Dushanbe areas varying between 10 and 60%. Representative samples from symptomatic plants tested positive for Potato virus Y (PVY) using virus-specific immunostrips (Agdia Inc., Elkhart, IN). Leaf samples from symptomatic plants were collected from Buston and Dushanbe areas, imprinted on FTA Classic Cards (Whatman International Ltd., Maidstone, UK), air dried, and shipped to the lab at Washington State University for confirmatory diagnostic tests. Total nucleic acids were eluted from FTA cards (1) and subjected to reverse transcription (RT)-PCR with primers (PVY/Y4A and PVY/Y3S) specific to the coat protein of PVY (3). Samples infected with PVY ordinary strain (PVYO), tuber necrosis strain (PVYNTN), tobacco veinal necrosis strains (PVYEU-N and PVYNA-N), and a recombinant strain (PVYN:O) were included as references to validate RT-PCR results. A single DNA product of approximately 480 bp was amplified from potato samples that tested positive with PVY-specific immunostrips. The amplified fragments from two samples from Dushanbe and six from Buston areas were cloned separately into pCR2.1 (Invitrogen Corp., Carlsbad, CA) and two independent clones per amplicon were sequenced from both orientations. Pairwise comparison of these sequences showed 90 to 100% identity among the cloned amplicons (GenBank Accession Nos. JQ743609 to JQ743616) and 90 to 100% with corresponding nucleotide sequence of reference PVY strains (GenBank Accession Nos. JQ743617 to JQ743621). A global phylogenetic analysis of sequences revealed the presence of PVYO in both samples from Dushanbe and one sample from Buston regions and presence of PVYNTN in the remaining five samples from the Buston region. Because of the possible occurrence of mixed infections of PVY strains (2), further studies are needed to determine the presence of mixed infections of two or more strains of PVY and their specificity to potato cultivars. To our knowledge, this study represents the first confirmed report of two distinct strains of PVY in potato in Tajikistan. The occurrence of PVYNTN, a quarantine pathogen in many countries (2), warrants additional investigations to improve sanitary status of potato fields and to facilitate the availability of virus-free seed in clean plant programs for significant yield increases in Tajikistan. References: (1) O. J. Alabi et al. J. Virol. Methods 154:111, 2008. (2) S. Gray et al. Plant Dis. 94:1384, 2010. (3) R. P. Singh et al. J. Virol. Methods 59:189, 1996.

Sign in / Sign up

Export Citation Format

Share Document