Molecular characterization of potato virus YN isolates by PCR-RFLP

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

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Molecular characterization of potato virus Y resistance in potato (Solanum tuberosumL.)

Indian Journal of Genetics and Plant Breeding (The) ◽

10.5958/0975-6906.2015.00062.0 ◽

2015 ◽

Vol 75 (3) ◽

pp. 389 ◽

Cited By ~ 2

Author(s):

Vinay Bhardwaj ◽

Reena Sharma ◽

Dalamu ◽

A. K. Srivastava ◽

R. Baswaraj ◽

...

Keyword(s):

Molecular Characterization ◽

Potato Virus ◽

Potato Virus Y

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Molecular Characterization of Potato leafroll virus, Potato virus A, and Potato virus X Isolates from Potatoes in Alaskan Cities and Villages

Plant Health Progress ◽

10.1094/php-2011-0209-01-br ◽

2011 ◽

Vol 12 (1) ◽

pp. 39 ◽

Cited By ~ 2

Author(s):

Nancy L. Robertson ◽

Jeffrey Smeenk ◽

Jodie M. Anderson

Keyword(s):

Molecular Characterization ◽

Potato Virus ◽

Potato Virus X ◽

Potato Leafroll Virus ◽

First Report ◽

Potato Virus A ◽

Potato Viruses ◽

The World ◽

Leafroll Virus

Although all three viruses are commonly found in potatoes throughout the world, this is the first report of potato viruses from Alaska to be sequenced and molecularly analyzed for comparisons with known viruses. Accepted for publication 17 January 2011. Published 9 February 2011.

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Molecular Analysis of Aquaglyceroporin 1 Gene in Non-Healing Clinical Iso¬lates Obtained from Patients with Cutaneous Leishmaniasis from Central of Iran

Journal of Arthropod-Borne Diseases ◽

10.18502/jad.v13i2.1240 ◽

2019 ◽

Author(s):

Yasaman Alijani ◽

Saeedeh Sadat Hosseini ◽

Salman Ahmadian ◽

Sonia Boughattas ◽

Gilda Eslami ◽

...

Keyword(s):

Gene Expression ◽

Cutaneous Leishmaniasis ◽

Molecular Characterization ◽

Significance Level ◽

Detection And Identification ◽

Pcr Rflp ◽

Leishmania Spp ◽

Sensitive Isolate ◽

The One

Background: Regarding the antimonial-resistant of Leishmania spp., understanding of related mechanism is necessary. One of the most important involved molecules is aquaglyceropin1 (AQP1). The aim of this study was molecular analysis of AQP1 gene from antimonial-resistant clinical isolates and its expression. Methods: Overall, 150 patients with cutaneous leishmaniasis referring to the reference laboratories of Yazd and Varzaneh,, located 105km southeast of Isfahan and 240km away from Yazd, were assessed from Jun 2015 to Dec 2017. After sampling, staining was done and evaluated for Leishman by microscope. Samples were collected in RNAlater solution for gene expression analysis in non-healing isolates. DNA extraction was performed from each slide with Leishman body. All patients with L. major isolates detected by ITS1-PCR-RFLP were followed for finding the resistant isolates, consequence of molecular characterization of AQP1 using PCR-RFLP. Gene expression of AQP1 from all resistant isolates was assessed in comparison with the one in a sensitive isolate. Statistical analysis was done using SPSS. The significance level was considered ≤0.05. Results: Five isolates were detected as antimonial resistant. Molecular detection and identification were appeared that all were L. major. The molecular characterization of AQP1 showed G562A mutation. Gene expression of AQP1 in resistant isolates showed 1.67 fold higher than the sensitive isolate. Conclusion: We reported a new point mutation of G562A in AQP1 gene involved in molecular mechanism in resistant isolates.

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Molecular characterization of Ovar-DRB1 exon2 gene in Garole sheep resilient to gastrointestinal nematodes

Indian Journal of Animal Research ◽

10.18805/ijar.6710 ◽

2015 ◽

Author(s):

C. Paswan ◽

L. L.L. Prince ◽

R. Kumar ◽

C. P. Swarnkar ◽

D. Singh ◽

...

Keyword(s):

Disease Resistance ◽

Molecular Characterization ◽

Molecular Mechanisms ◽

Gastrointestinal Nematodes ◽

Exon 2 ◽

Pcr Rflp

Ovine MHC DRB1 exon 2 (Ovar-DRB1.2) gene is arguably one of the critical genes, responsible for disease resistance against parasite in animals. This study was carried out for indepth analysis of polymorphism in MHC DRB1.2 gene and to explore the underlying molecular mechanisms for the development of disease resistance in Garole. PCR-RFLP study revealed that the gene is polymorphic in nature. The frequency of allele ‘A’ for endonuclease SacI and Allele ‘B’ for endonuclease Hin1I were significantly higher in Garole population.

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Molecular characterization of 'Candidatus Phytoplasma solani' in celery: Case study in Futog

Ratarstvo i povrtarstvo ◽

10.5937/ratpov58-33227 ◽

2021 ◽

Vol 58 (2) ◽

pp. 66-71

Author(s):

Tatjana Popović ◽

Petar Mitrović ◽

Andrea Kosovac

Keyword(s):

Molecular Characterization ◽

Gene Detection ◽

Convolvulus Arvensis ◽

Visual Evaluation ◽

Leaf Yellowing ◽

Pcr Rflp ◽

Novi Sad ◽

Stolbur Phytoplasma

'Candidates Phytoplasma solani', known by its trivial name stolbur phytoplasma, is a plant pathogen infecting numerous crops in Serbia. Celery plants with prominent leaf yellowing and chlorosis, sporadically with tissue necrosis, were observed during August 2020 in Futog, situated in Novi Sad suburbia in Vojvodina. Total of 12 sampled celery plants, 8 symptomatic and 4 asymptomatic ones, were analysed for 'Ca. P. solani' presence. All symptomatic celery plants were infected with stolbur phytoplasma according to the stoll 1 gene detection and therefore were further subjected to multigene molecular characterization on three genes: tuf, stamp and vmpl. Combining molecular tools PCR/RFLP and sequencing reviled two 'Ca. P. solani' multilocus genotypes in celery: tuf-b/Rqg31/V14 and tuf-b/ Rpm35/V14, present in 4 samples each. Obtained results of the strain genotyping are in concordance with previous data on the 'Ca. P. solani' diversity on celery, but supplemented with genotyping of the vmpl gene. Outbreak of stolbur phytoplasma in the assessed locality in Futog is linked to tuf-b epidemiological cycle correlated in Serbia mainly with weed Convolvulus arvensis which was present in the subjected celery plot, and could have been the phytoplasma inoculum source. Visual evaluation of the symptom occurrence suggests on 10-15% of 'Ca. P. solani' affected celery plants scattered throughout the plot corresponding to the pathogen dispersal in crop by cixiid planthoper Hyalesthes obsoletus (Hemiptera: Auchenorrhyncha) associated with C. arvensis, main vector of stolbur phytoplasma in Serbia.

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Identification and Molecular Characterization of Recombinant Potato Virus Y (PVY) in Potato from South Korea, PVYNTN Strain

Plant Disease ◽

10.1094/pdis-05-18-0715-re ◽

2019 ◽

Vol 103 (1) ◽

pp. 137-142 ◽

Cited By ~ 3

Author(s):

Mohamad Chikh-Ali ◽

Mariana Rodriguez-Rodriguez ◽

Kelsie J. Green ◽

Dong-Jun Kim ◽

Sang-Min Chung ◽

...

Keyword(s):

South Korea ◽

Whole Genome Sequencing ◽

Molecular Characterization ◽

Genome Sequencing ◽

Potato Virus ◽

Potato Virus Y ◽

Potato Production ◽

Whole Genome ◽

Rt Pcr

Potato is an important source of food in South Korea, and viruses represent a significant threat to sustainable and profitable potato production. However, information about viruses affecting the potato crop in South Korea is limited. In 2017, potato plants of five cultivars exhibiting foliar mosaic, crinkling, and mottle were collected in two seed potato production areas, in Gangwon-do and Jeollabuk-do Provinces, and subjected to virus testing and characterization. Potato virus Y (PVY) was found associated with mosaic symptoms, and samples were characterized using reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing. All analyzed PVY-positive samples were found to represent the same recombinant PVY strain: PVYNTN. Three PVY isolates were subjected to whole genome sequencing using overlapping RT-PCR fragments and Sanger methodology, and all three were confirmed to represent strain PVYNTNa after a recombination analysis of the complete genomes. In phylogenetic analysis, the three South Korean isolates were placed most closely to several PVYNTNa isolates reported from Japan and Vietnam, suggesting a common source of infection. This is the first report and complete molecular characterization of a PVYNTN strain present in the country, and because this strain induces tuber necrotic ringspot disease in susceptible cultivars of potato, appropriate management tools need to be implemented to mitigate potential tuber quality losses.

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Molecular Characterization of Potato virus V Genomes from Europe Indicates Limited Spatiotemporal Strain Differentiation

Phytopathology ◽

10.1094/phyto.2000.90.4.437 ◽

2000 ◽

Vol 90 (4) ◽

pp. 437-444 ◽

Cited By ~ 22

Author(s):

Igor Oruetxebarria ◽

Tuija Kekarainen ◽

Carl Spetz ◽

Jari P. T. Valkonen

Keyword(s):

Phylogenetic Analysis ◽

Molecular Characterization ◽

Potato Virus ◽

Genomic Sequence ◽

Host Responses ◽

Single Strain ◽

Reading Frame ◽

Solanaceae Species ◽

Nontranslated Region

Because there were no previous reports on the molecular characterization of Potato virus V (PVV, genus Potyvirus, family Potyviridae), the complete genomic sequence of PVV isolate Dv42 was determined. The length of the single-stranded messenger-polarity RNA genome was 9,851 nt (nucleotides), followed by a poly(A) tail. The genome contained a 5′-terminal nontranslated region (5′-NTR; 204 nt), a single open reading frame (nucleotides 205-9406; 3,067 amino acids), and a 3′-NTR that was unusually long (446 nt) compared with that of Potato virus Y (PVY; 331-nt 3′-NTR), Potato virus A (PVA; 207-nt 3′-NTR), and other potyviruses that naturally infect Solanaceae species. Phylogenetic analysis with the cylindrical inclusion protein-encoding and coat protein (CP)-encoding regions indicated that PVV Dv42 was most closely related to Pepper mottle virus and PVY, respectively. Seven PVV isolates (including Dv42) collected from cultivated potatoes in the Netherlands, the United Kingdom, and Norway from 1964 to 1997 were uniform in serological properties and symptomatology in indicator hosts that could distinguish strains of PVY and PVA. The nucleotide sequences of the 5′-NTR, P1, CP, and 3′-NTR regions of the PVV isolates were determined and were 94.6 to 99.5, 96.3 to 98.8, 96.4 to 98.7, and 96.3 to 99.6% identical, respectively. The amino acid similarities for the P1 and CP were 95.8 to 98.6 and 96.0 to 97.8%, respectively. Phylogenetic analysis of the CP sequences of PVV revealed no significant grouping, in contrast to PVY and PVA, which were grouped largely according to the previously recognized strains based on host responses. However, the relatively few differences in the P1 sequences of PVV were correlated with the different countries of origin. Hence, the PVV isolates infecting potatoes in Europe seem to vary little genetically and may belong to a single strain.

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