Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Glasa M

PROVIDER: S-EPMC8069754 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains.

Project description:The ordinary strain of Potato virus Y (PVY), PVY(O), causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny gene. A novel substrain of PVY(O) was recently reported, PVY(O)-O5, which is spreading in the United States and is distinguished from other PVY(O) isolates serologically (i.e., reacting to the otherwise PVY(N)-specific monoclonal antibody 1F5). To characterize this new PVY(O)-O5 subgroup and address possible reasons for its continued spread, we conducted a molecular study of PVY(O) and PVY(O)-O5 isolates from a North American collection of PVY through whole-genome sequencing and phylogenetic analysis. In all, 44 PVY(O) isolates were sequenced, including 31 from the previously defined PVY(O)-O5 group, and subjected to whole-genome analysis. PVY(O)-O5 isolates formed a separate lineage within the PVY(O) genome cluster in the whole-genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. On the other hand, the PVY(O) sequences separated into at least two distinct lineages on the whole-genome phylogenetic tree. To shed light on the origin of the three most common PVY recombinants, a more detailed phylogenetic analysis of a sequence fragment, nucleotides 2,406 to 5,821, that is present in all recombinant and nonrecombinant PVY(O) genomes was conducted. The analysis revealed that PVY(N:O) and PVY(N-Wi) recombinants acquired their PVY(O) segments from two separate PVY(O) lineages, whereas the PVY(NTN) recombinant acquired its PVY(O) segment from the same lineage as PVY(N:O). These data suggest that PVY(N:O) and PVY(N-Wi) recombinants originated from two separate recombination events involving two different PVY(O) parental genomes, whereas the PVY(NTN) recombinants likely originated from the PVY(N:O) genome via additional recombination events.

| S-EPMC3251920 | biostudies-literature

Transcriptome profiling of potato hypersensistive response to PVY infection

Project description:Our aim was to investigate involvement of salicylic acid signalling in Ny-mediated hypersensistive response by comparison of transcriptomic response to the Potato Virus Y in potato plants of genotypes Rywal, bearing Ny-1 allele and NahG-Rywal, unable to accumulate salicylic acid in three time points (1, 3 and 6 days post inoculation) after viral inoculation.

2013-10-01 | GSE46180 | GEO

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints.

Project description:The study of the 3D architecture of chromosomes has been advancing rapidly in recent years. While a number of methods for 3D reconstruction of genomic models based on Hi-C data were proposed, most of the analyses in the field have been performed on different 3D representation forms (such as graphs). Here, we reproduce most of the previous results on the 3D genomic organization of the eukaryote Saccharomyces cerevisiae using analysis of 3D reconstructions. We show that many of these results can be reproduced in sparse reconstructions, generated from a small fraction of the experimental data (5% of the data), and study the properties of such models. Finally, we propose for the first time a novel approach for improving the accuracy of 3D reconstructions by introducing additional predicted physical interactions to the model, based on orthologous interactions in an evolutionary-related organism and based on predicted functional interactions between genes. We demonstrate that this approach indeed leads to the reconstruction of improved models.

| S-EPMC4441392 | biostudies-literature

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

Project description:Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of plant immunity is therefore economically important, guiding the enforcement of crop resistance. To disentangle complex regulatory mechanisms of the plant immune responses, understanding system as a whole is a must. However, integrating data from different molecular analysis (transcriptomics, proteomics, metabolomics, smallRNA regulation etc.) is not straightforward. We evaluated the response of potato (Solanum tuberosum L.) following the infection with potato virus Y (PVY). The response has been analyzed on two molecular levels, with microarray transcriptome analysis and mass spectroscopy-based proteomics. Within this report, we performed detailed analysis of the results on both levels and compared two different approaches for analysis of proteomic data (spectral count versus MaxQuant). To link the data on different molecular levels, each protein was mapped to the corresponding potato transcript according to StNIB paralogue grouping. Only 33% of the proteins mapped to microarray probes in a one-to-one relation and additionally many showed discordance in detected levels of proteins with corresponding transcripts. We discussed functional importance of true biological differences between both levels and showed that the reason for the discordance between transcript and protein abundance lies partly in complexity and structure of biological regulation of proteome and transcriptome and partly in technical issues contributing to it.

| S-EPMC5620531 | biostudies-literature

Local and systemic gene expression in potato infected with PVY

Project description:The goal of these studies is analysis of gene expression profiles in potato plants infected with potato virus Y (necrotic strain - PVYN). A prototypic plant pathogen interaction system used to study disease resistance is tobacco (Nicotiana tabacum) and tobacco mosaic virus (TMV). In tobacco, the resistance response comprises two phenomena, known as the hypersensitive response (HR) and systemic acquired resistance (SAR). HR is typically characterized by a local necrosis surrounding the site of viral entry leading to restriction of pathogen replication and spread. SAR is the enhanced ability of the plant to resist a secondary challenge by the same or a different pathogen inoculated elsewhere on the plant. The identity of the signal(s) that induces HR and SAR is still poorly understood. Plants of S. tuberosum cv. Rywal, resistant to all known (N, 0, NTN) PVY strains, were grown in growth chambers using 16 h period of light (22°C) and 8 h of darkness (18°C). For all experiments, 6-week-old plants were used. For inoculation with PVY, carborundum-dusted leaves were rubbed with water (mock control) or PVYN solution (1 µg ml-1). Two to four leaves were inoculated on each plant and harvested together at 1, 3, and 6 days post inoculation (dpi). Separately, noninoculated leaves were harvested at the same time points (upper leaves). The first time point (1 dpi) has been chosen to study the early stage of plant response before necrotic lesion formation. At 3 dpi necrotic lesions start to appear, and at 6 dpi necroses are fully developed which correlates with the maximum of salicylic acid increase in virus inoculated leaves. Keywords: Direct comparison

2008-02-13 | GSE10488 | GEO

Early response of potato plants to virus (PVY-NTN) inoculation

Project description:Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. The cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN interaction. Differential gene expression in early response of potato cv. Igor plants to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 12 hours after inoculation, in four biological replicates. Keywords: direct comparison

2008-03-21 | GSE10903 | GEO

Effect of two potato viruses, PLRV and PVY, on potato gene expression in Russet Burbank

Project description:Potato plants (cv. Russet Burbank) were grown as in vitro plantlets, and transplanted into 12-cm pots in Sunshine Mix #2 (peat/perlite mix) supplemented with slow release fertilizer (Osmocoat) in the greenhouse. The experiment was conducted in the summer of 2004 at Moscow, ID. Plantings were staggered to facilitate collection of volatiles and leaf samples during a short harvest window for all times of all treatments. Infectious Green Peach Aphids were raised on PLRV-infected potato plants; test plants were infected by placing 10 infectious aphids on a leaf in a clip cage for 48 h. The control plants for PLRV were similarly treated with aphids that had been raised on uninfected potato plants. A local isolate of PVYO was inoculated mechanically using purified virus (5 ìg ml-1) in buffer (50 mM Na2HPO4, 20 mM Na2SO3 pH 7.0) lightly rubbed onto a leaf previously dusted with carborundum. Control plants for PVY were treated in the same manner using buffer without PVY. The RNA samples were made from systemically affected leaves, excluding the actual leaves inoculated by aphids or that received the mechanical infection. Leaf volatiles were concurrently collected from equivalent plants; aliquots of frozen leaf samples were sent for metabolite analysis prior to RNA extraction. Leaf harvests were made 1, 3, 7, 14, and 28 d post-inoculation. Keywords: Direct comparison

2007-09-01 | GSE8213 | GEO

Distribution and molecular characterization of potato virus Y (PVY) strains infecting potato (<i>Solanum tuberosum</i>) crop in Kashmir (India).

Project description:For breeding resistant cultivars, understanding the nature and distribution of PVY strains is indispensable. In present study, during the course of survey two hundred potato samples showing symptoms of vein clearing, mosaic, stunting, mottling, curling and vein banding were collected from 4 major potato growing districts of Kashmir valley. The disease incidence ranged from 16 to 27.33% with maximum in district Srinagar (27.33%). All the samples were serologically tested for PVY infection using DAS-ELISA and 74 tested positive for PVY infection. Out of 74 positive samples forty samples were re-confirmed by RT-PCR by amplifying 900 bp using coat protein (CP) gene specific primers. The PCR-positive samples were further characterized into different strains using strain specific primers. The strains NTN, N and O were reported and among them NTN strain was found to be most prevalent throughout the valley. The phylogenetic analysis of selected isolates carried out with known PVY strains also confirmed that the isolates belong to the N, NTN and O strains of PVY. The study will help in developing point of care strain specific diagnostics and also in devising the strategy for developing PVY resistant varieties, because when we have the complete information about the virus and its strains it will help us in screening the germplasm against each strain and, therefore, eventually development of a multi-strain resistant variety.Supplementary informationThe online version contains supplementary material available at 10.1007/s13337-021-00722-2.

| S-EPMC8630282 | biostudies-literature

Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants.

Project description:Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe. PVY reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in the PVY genome. The PVY genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:CI, NIa, NIb-Pro, HC-Pro, CP, and VPg. A total of 343 mature miRNAs were retrieved from the miRBase database and were examined for their target sequences in PVY genes using the minimum free energy (mfe), minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. The identified potato miRNAs against viral mRNA targets have antiviral activities, leading to translational inhibition by mRNA cleavage and/or mRNA blockage. We found 86 miRNAs targeting the PVY genome at 151 different sites. Moreover, only 36 miRNAs potentially targeted the PVY genome at 101 loci. The CI gene of the PVY genome was targeted by 32 miRNAs followed by the complementarity of 26, 19, 18, 16, and 13 miRNAs. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h, and miR5303d) that could target the CI, NIa, NIb-Pro, HC-Pro, CP, and VPg genes of PVY. The predicted miRNAs can be used for the development of PVY-resistant potato crops in the future.

| S-EPMC5022016 | biostudies-literature

Global Screening and Functional Identification of Major HSPs Involved in PVY Infection in Potato.

Project description:HSP40 (also known as DnaJ), HSP70, and HSP90 are major heat shock protein (HSP) families that play critical roles in plant growth and development and stress adaption. Recently, several members of the three HSP families were reported to be widely involved in the plant host-virus interactions. However, their global expression profiles and core members recruited by viruses are largely unknown. In this study, a total of 89 StDnaJs were identified from a genome-wide survey, and their classification, phylogenetic relationships, chromosomal locations, and gene duplication events were further analyzed. Together with 20 StHSP70s and 7 StHSP90s previously identified in the potato genome, the global expression patterns of the members in 3 HSP families were investigated in 2 potato cultivars during Potato virus Y (PVY) infection using RNA-seq data. Of them, 16 genes (including 8 StDnaJs, 6 StHSP70s, and 2 StHSP90s) were significantly up- or downregulated. Further analysis using qRT-PCR demonstrated that 7 of the 16 genes (StDnaJ06, StDnaJ17, StDnaJ21, StDnaJ63, StHSP70-6, StHSP70-19, and StHSP90.5) were remarkably upregulated in the potato cultivar 'Eshu 3' after PVY infection, implying their potential roles in the potato-PVY compatible interaction. Subsequent virus-induced gene silencing (VIGS) assays showed that silencing of the homologous genes of StDnaJ17, StDnaJ21, StHSP70-6, and StHSP90.5 in Nicotiana. benthamiana plants dramatically reduced the accumulation of PVY, which indicated the four genes may function as susceptibility factors in PVY infection. This study provides candidate genes for exploring the mechanism of potato-PVY compatible interaction and benefits breeding work aiming to produce new cultivars with the ability to grow healthily under PVY infection.

| S-EPMC9031240 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data