scholarly journals Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan

2023 ◽  
Vol 83 ◽  
Author(s):  
M. Ahsan ◽  
M. Ashfaq ◽  
H. Riaz ◽  
Z. Khan ◽  
M. Z. Hamza ◽  
...  
Keyword(s):  
Spinacia Oleracea ◽  
Balancing Selection ◽  
Statistical Tests ◽  
Disease Incidence ◽  
Phylogenetic Reconstruction ◽  
Enzyme Linked Immunosorbent Assay ◽  
Subgroup Ii ◽  
Cmv Disease ◽  
Indel Event

Abstract Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour-joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity (π) of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 <0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the values 2.02535, 0.01468, and 0.71862 of Tajima's D, Fu, & Li’s F* and D* respectively, demonstrating that the CMV population is under balancing selection.

scholarly journals Molecular Characterization of the Begomovirus Associated Satellites Infecting Spinacia Oleracea and Capsicum Annum Plants in Kohat, Pakistan

2020 ◽  
Vol 2 (4) ◽  
pp. 43-56
Author(s):  
Malik Nawaz Shuja
Keyword(s):  
Spinacia Oleracea ◽  
Sequence Similarity ◽  
Disease Incidence ◽  
Tomato Leaf ◽  
Capsicum Annum ◽  
Wide Range ◽  
Dna 2 ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Begomovirus is a major and economically important genus of the Geminiviridae family. It comprises a wide range of viruses that infect a number of dicot plants including the horticulture crops, cereal crops, aromatic plants, vegetable crops, medicinal plants and weeds in various regions of the world. This study aims to investigate and correlate the various symptoms of begomovirus / satellites in different plants grown in the vicinity of Kohat, Pakistan. Furthermore, the characterization of the selected virus-associated satellites at the molecular level is also studied. Samples of suspected plants showing begomoviral infection were collected from the Kohat District. Genomic DNA was extracted from the infected plants and subjected to PCR using DNA-1/DNA-2 and Beta01/Beta02 for alpha satellites and beta satellites, respectively. The amplified PCR products were cloned and sequenced commercially. After sequencing, in silico sequence and phylogenetic analysis was also performed. Our study discovered that many plants in the Kohat District display begomovirus and satellite disease symptoms with mild to extreme disease severity. Disease incidence is especially high in okra. Beta satellites were isolated and sequenced from Spinacia oleracea and Capsicum annum plants and they showed more than 90% sequence similarity with chilli leaf curl and tomato leaf curl beta satellites. The existence of betasatellites in spinach and chilli plants was discovered for the first time in the Kohat region. Moreover, the distribution of these highly pathogenic variants of chilli leaf curl and tomato leaf curl betasatellites in the district Kohat has been reported previously. 

scholarly journals Biological, Serological, and Molecular Characterization of a Highly Divergent Strain of Grapevine leafroll-associated virus 4 Causing Grapevine Leafroll Disease

2015 ◽  
Vol 105 (9) ◽  
pp. 1262-1269 ◽  
Author(s):  
Jean-Sébastien Reynard ◽  
Pierre H. H. Schneeberger ◽  
Jürg Ernst Frey ◽  
Santiago Schaerer
Keyword(s):  
Large Scale ◽  
Amino Acid Identity ◽  
Biological Properties ◽  
Enzyme Linked Immunosorbent Assay ◽  
Subgroup Ii ◽  
Leafroll Disease ◽  
Serological Data ◽  
Pyrosequencing Technology ◽  
Divergent Strain

The complete genome sequence of a highly divergent strain of Grapevine leafroll-associated virus 4 (GLRaV-4) was determined using 454 pyrosequencing technology. This virus, designated GLRaV-4 Ob, was detected in Vitis vinifera ‘Otcha bala’ from our grapevine virus collection at Agroscope. The GLRaV-4 Ob genome length and organization share similarities with members of subgroup II in the genus Ampelovirus (family Closteroviridae). Otcha bala was graft-inoculated onto indicator plants of cultivar Gamay to evaluate the biological properties of this new strain, and typical leafroll symptoms were induced. A monoclonal antibody for the rapid detection of GLRaV-4 Ob by enzyme-linked immunosorbent assay is available, thus facilitating large-scale diagnostics of this virus. Based on the relatively small size of the coat protein, the reduced amino acid identity and the distinct serological properties, our study clearly shows that GLRaV-4 Ob is a divergent strain of GLRaV-4. Furthermore, molecular and serological data revealed that the AA42 accession from which GLRaV-7 was originally reported is in fact co-infected with GLRaV-4 Ob and GLRaV-7. This finding challenges the idea that GLRaV-7 is a leafroll-causing agent.

scholarly journals Molecular Characterization of the Begomovirus Associated Satellites Infecting Spinacia Oleracea and Capsicum Annum Plants in Kohat, Pakistan

2020 ◽  
Vol 2 (4) ◽  
pp. 43-56
Author(s):  
Ali Shah ◽  
Ayesha Ayub ◽  
Malik Nawaz Shuja ◽  
Taj Ali ◽  
Fazal Akbar
Keyword(s):  
Spinacia Oleracea ◽  
Sequence Similarity ◽  
Disease Incidence ◽  
Tomato Leaf ◽  
Capsicum Annum ◽  
Wide Range ◽  
Dna 2 ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Begomovirus is a major and economically important genus of the Geminiviridae family. It comprises a wide range of viruses that infect a number of dicot plants including the horticulture crops, cereal crops, aromatic plants, vegetable crops, medicinal plants and weeds in various regions of the world. This study aims to investigate and correlate the various symptoms of begomovirus / satellites in different plants grown in the vicinity of Kohat, Pakistan. Furthermore, the characterization of the selected virus-associated satellites at the molecular level is also studied. Samples of suspected plants showing begomoviral infection were collected from the Kohat District. Genomic DNA was extracted from the infected plants and subjected to PCR using DNA-1/DNA-2 and Beta01/Beta02 for alpha satellites and beta satellites, respectively. The amplified PCR products were cloned and sequenced commercially. After sequencing, in silico sequence and phylogenetic analysis was also performed. Our study discovered that many plants in the Kohat District display begomovirus and satellite disease symptoms with mild to extreme disease severity. Disease incidence is especially high in okra. Beta satellites were isolated and sequenced from Spinacia oleracea and Capsicum annum plants and they showed more than 90% sequence similarity with chilli leaf curl and tomato leaf curl beta satellites. The existence of betasatellites in spinach and chilli plants was discovered for the first time in the Kohat region. Moreover, the distribution of these highly pathogenic variants of chilli leaf curl and tomato leaf curl betasatellites in the district Kohat has been reported previously. 

TBE in Sweden

2020 ◽  
Keyword(s):  
Genetic Characterization ◽  
Immunoglobulin M ◽  
Enzyme Linked Immunosorbent Assay ◽  
Second Phase ◽  
Serum Samples ◽  
Tick Borne Encephalitis ◽  
Specific Immunoglobulin ◽  
Tick Borne Encephalitis Virus ◽  
First Time

Tick-borne encephalitis virus (TBEV) was isolated for the first time in Sweden in 1958 (from ticks and from 1 tick-borne encephalitis [TBE] patient).1 In 2003, Haglund and colleagues reported the isolation and antigenic and genetic characterization of 14 TBEV strains from Swedish patients (samples collected 1991–1994).2 The first serum sample, from which TBEV was isolated, was obtained 2–10 days after onset of disease and found to be negative for anti-TBEV immunoglobulin M (IgM) by enzyme-linked immunosorbent assay (ELISA), whereas TBEV-specific IgM (and TBEV-specific immunoglobulin G/cerebrospinal fluid [IgG/CSF] activity) was demonstrated in later serum samples taken during the second phase of the disease.

scholarly journals Purification and initial characterization of the proteasome from the higher plant Spinacia oleracea.

1992 ◽  
Vol 267 (30) ◽  
pp. 21678-21684 ◽  
Author(s):  
M Ozaki ◽  
K Fujinami ◽  
K Tanaka ◽  
Y Amemiya ◽  
T Sato ◽  
...  
Keyword(s):  
Spinacia Oleracea ◽  
Higher Plant ◽  
Initial Characterization

scholarly journals Incidence and distribution of Sweetpotato viruses and their implication on sweetpotato seed system in Malawi

2021 ◽  
Author(s):  
Willard Mbewe ◽  
Andrew Mtonga ◽  
Margret Chiipanthenga ◽  
Kennedy Masamba ◽  
Gloria Chitedze ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Virus Disease ◽  
Disease Incidence ◽  
Mottle Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Foliar Symptoms ◽  
Membrane Enzyme ◽  
Sweet Potato Virus ◽  
Seed System ◽  
Clean Seed

AbstractA survey was carried out in 19 districts to investigate the prevalence and distribution of sweetpotato virus disease (SPVD) and its implication on the sustainability of clean seed system in Malawi. A total of 166 leaf samples were collected and tested for the presence of 8 viruses using nitrocellulose membrane enzyme-linked immunosorbent assay (NCM-ELISA). SPVD foliar symptoms were observed in 68.42% of the surveyed districts. There were significant variations in disease incidence and severity (p < 0.001) among districts, with the highest incidence in Mulanje (28.34%). Average SPVD severity score was 3.05. NCM-ELISA detected sweet potato feathery mottle virus (SPFMV, 30.54%), sweet potato mild mottle virus (SPMMV, 31.14%), sweet potato mild speckling virus (SPMSV, 16.17%), sweet potato C-6 virus (SPC6V, 13.77%), sweet potato chlorotic stunt virus (SPCSV, 22.16%), sweet potato collusive virus (SPCV, 30.54%), sweet potato virus G (SPVG, 11.38%), cucumber mosaic virus (CMV, 7.78%) either in single or mixed infections. Data from this study indicate a significant SPVD occurrence in the country, and the consequence implications towards national sweetpotato seed system.

scholarly journals Characterization of Gnomoniopsis idaeicola, the Causal Agent of Canker and Wilting of Blackberry in Serbia

Plant Disease ◽  
2019 ◽  
Vol 103 (2) ◽  
pp. 249-258 ◽  
Author(s):  
Miloš Stevanović ◽  
Danijela Ristić ◽  
Svetlana Živković ◽  
Goran Aleksić ◽  
Ivana Stanković ◽  
...  
Keyword(s):  
Disease Incidence ◽  
Initial Step ◽  
First Record ◽  
Wide Distribution ◽  
Causal Agent ◽  
Control Measures ◽  
Molecular Features ◽  
Intraspecies Diversity ◽  
Specific Symptoms

Blackberry cane diseases with the symptoms of necrosis, canker, and wilting are caused by several fungi worldwide. Surveys conducted from 2013 to 2016 in Serbia revealed the occurrence of Gnomoniopsis idaeicola, the causal agent of cane canker and wilting, which was found to be distributed in almost half of the surveyed orchards, in three blackberry cultivars, and with disease incidence of up to 80%. Wide distribution and high disease incidence suggest that G. idaeicola has been present in Serbia for some time. Out of 427 samples, a total of 65 G. idaeicola isolates were obtained (isolation rate of 34.19%). Reference isolates, originating from different localities, were conventionally and molecularly identified and characterized. G. idaeicola was detected in single and mixed infections with fungi from genera Paraconiothyrium, Colletotrichum, Diaporthe, Botryosphaeria, Botrytis, Septoria, Neofusicoccum, and Discostroma, and no diagnostically specific symptoms could be related directly to the G. idaeicola infection. In orchards solely infected with G. idaeicola, blackberry plant mortality was up to 40%, and yield loses were estimated at 50%. G. idaeicola isolates included in this study demonstrated intraspecies diversity in morphological, biological, pathogenic, and molecular features, which indicates that population in Serbia may be of different origin. This is the first record of a massive outbreak of G. idaeicola infection, illustrating its capability of harmful influence on blackberry production. This study represents the initial step in studying G. idaeicola as a new blackberry pathogen in Serbia, aiming at developing efficient control measures.

scholarly journals Use of Quantitative Molecular Diagnostic Assays to Investigate Fusarium Dry Rot in Potato Stocks and Soil

2005 ◽  
Vol 95 (12) ◽  
pp. 1462-1471 ◽  
Author(s):  
D. W. Cullen ◽  
I. K. Toth ◽  
Y. Pitkin ◽  
N. Boonham ◽  
K. Walsh ◽  
...  
Keyword(s):  
Control Strategies ◽  
Disease Incidence ◽  
Harvest Date ◽  
Molecular Diagnostic ◽  
Enzyme Linked Immunosorbent Assay ◽  
Potato Seed ◽  
Fusarium Spp ◽  
Dry Rot ◽  
Diagnostic Assays ◽  
Final Harvest

Specific and sensitive quantitative diagnostics, based on real-time (TaqMan) polymerase chain reaction (PCR) and PCR enzyme-linked immunosorbent assay, were developed to detect dry-rot-causing Fusarium spp. (F. avenaceum, F. coeruleum, F. culmorum, and F. sulphureum). Each assay detected Fusarium spp. on potato seed stocks with equal efficiency. Four potato stocks, sampled over two seed generations from Scottish stores, were contaminated with F. avenaceum, F. sulphureum, F. culmorum, F. coeruleum or a combination of species, and there was a general trend towards increased Fusarium spp. contamination in the second generation of seed sampled. F. sulphureum and F. coeruleum caused significantly (P < 0.05) more disease in storage than the other species when disease-free tubers of potato cvs. Spunta and Morene were inoculated at a range of inoculum concentrations (0, 104, 105, and 106 conidia/ml). Increased DNA levels were correlated with increased disease severity between 8 and 12 weeks of storage. The threshold inoculum levels resulting in significant disease development on both cultivars were estimated to be 104 conidia/ml for F. sulphureum and 105 conidia/ml for F. coeruleum. To study the effect of soil infestation and harvest date on disease incidence, seed tubers of cvs. Morene and Spunta were planted in a field plot artificially infested with the four Fusarium spp. F. culmorum and F. sulphureum were detected in soil taken from these plots at harvest, and F. sulphureum DNA levels increased significantly (P < 0.05) at the final harvest. All four Fusarium spp. were detected in progeny tubers. There was a trend toward higher levels of F. culmorum detected in progeny tubers at the earliest harvest date, and higher levels of F. sulphureum at the final harvest. The use of diagnostic assays to detect fungal storage rot pathogens and implications for disease control strategies are discussed.

Prevalence and Molecular Characterization Coat Protein Gene of Tobacco streak virus Causing Peanut Stem Necrosis Disease in Coastal and Rayalaseema Districts of Andhra Pradesh, South-India

2021 ◽  
Author(s):  
K. Saratbabu ◽  
K. Vemana ◽  
A.K. Patibanda ◽  
B. Sreekanth ◽  
V. Srinivasa Rao
Keyword(s):  
Coat Protein ◽  
Molecular Characterization ◽  
Andhra Pradesh ◽  
Disease Incidence ◽  
Tobacco Streak Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Streak Virus ◽  
Rt Pcr ◽  
Cp Gene ◽  
Stem Necrosis

Background: Peanut stem necrosis disease (PSND) caused by Tobacco streak virus (TSV) is a major constraint for groundnut production in Andhra Pradesh (A.P.). However, studies on prevalence and spread of the disease confined to only few districts of A.P. with this background current study focused on incidence and spread of the disease in entire state of A.P. Further an isolate of TSV occurring in A.P. characterized on the basis of genetic features by comparing with other TSV isolates originated from different hosts and locations from world.Methods: Roving survey was conducted during kharif 2017-18 in groundnut growing districts of Andhra Pradesh (A.P.) for peanut stem necrosis disease incidence. Groundnut plants showing PSND symptoms were collected and tested with direct antigen coating enzyme linked immunosorbent assay (DAC-ELISA). Groundnut samples found positive by ELISA once again tested by reverse transcription polymerase chain reaction (RT-PCR). The representative TSV-GN-INDVP groundnut isolate from Prakasham district was maintained on cowpea seedlings by standard sap inoculation method in glasshouse for further molecular characterization. The Phylogenetic tree for coat protein (CP) gene was constructed using aligned sequences with 1000 bootstrap replicates following neighbor-joining phylogeny.Result: Thirty-eight (52.7%) of seventy-two groundnut samples collected from different locations in A.P were given positive reaction to TSV by DAC-ELISA. For the first time, PSND incidence observed in coastal districts (Krishna, Guntur, Sri Pottisriramulu Nellore, Prakasham) of A.P. Maximum PSND incidence recorded from Bathalapalli (22.2%) and the minimum incidence in Mulakalacheruvu (4.1%). The coat protein (CP) gene of TSV-GN-INDVP groundnut isolate was amplified by RT-PCR and it shared maximum per cent nucleotide identity (97.51-98.62%) with TSV isolates from groundnut and other different crops reported in India. All Indian isolates cluster together irrespective of crop and location based on the phylogenetic analysis.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

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