Single-Strand Conformation Polymorphism for Molecular Variability Studies of Six Viroid Species

Elleuch, Amine; Hamdi, I.; Bessaies, Nabiha; Fakhfakh, H.

doi:10.1271/bbb.120714

Cited by 8 publications

(7 citation statements)

References 23 publications

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“…The same authors also provided the first insights into the genetic variability of PBCVd through the identification of different sequence variants (using conventional Sanger sequencing) that revealed the quasiespecies nature of this viroid, as previously proposed for RNA viruses (Holland et al, 1982). A high number of point mutations affecting the PBCVd CCR have been reported (Ambros et al, 1995a;Yesilcollou et al, 2010), and many complete viroid variants from different isolates, hosts and geographic origin have been characterized Ambrós et al, 1995a;Joyce et al, 2006;Lolic et al, 2007;Kaponi et al, 2010;Yesilcollou et al, 2010;Nome et al, 2011;Elleuch et al, 2013), allowing the identification of 115 polymorphic positions distributed along the viroid genome and showing that the viroid size may range from 312 to 317 nt. Interestingly, most polymorphic positions map at loops and/or are compensatory mutations preserving the secondary structure foreseen for PBCVd (Fig.…”

Section: Pear Blister Canker Viroidmentioning

confidence: 66%

On the early identification and characterization of pear blister canker viroid, apple dimple fruit viroid, peach latent mosaic viroid and chrysanthemum chlorotic mottle viroid

et al. 2023

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Section: Pear Blister Canker Viroidmentioning

confidence: 66%

On the early identification and characterization of pear blister canker viroid, apple dimple fruit viroid, peach latent mosaic viroid and chrysanthemum chlorotic mottle viroid

et al. 2023

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“…Total RNA extractions were performed using the RNeasy Plant Mini kit (Qiagen) from 100 mg of petioles or veins of symptomatic leaves or adsorption of nucleic acids on silica particles from 1 g of grapevine tissues (Rott and Jelkmann 2001), grinding plant tissue in liquid nitrogen, and following the mentioned protocols. The primer pairs used to amplify GYSVd-1 for one-step RT-PCR were GYSVd-1-AS (5′-GCG GGG GTT CCG GGG ATT GC-3′) and GYSVd-1-S (5′-TAA GAG GTC TCC GGA TCT TCT TGC-3′), complementary and viral, respectively (Elleuch et al 2013). RT-PCR in a single step was carried out using the One Step RT-PCR kit (Qiagen) according to the manufacturer's instructions with 4 μL of total RNA.…”

Section: Methodsmentioning

confidence: 99%

Detection and molecular characterization of Grapevine yellow speckle viroid 1 isolates infecting grapevines in Brazil

Fajardo

Eiras

Nickel

2016

Trop. plant pathol.

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Presently, Hop stunt viroid (HSVd) and Citrus exocortis viroid (CEVd) are the only viroids reported to infect grapevines (Vitis spp.) in Brazil, among the seven viroid species already reported infecting this host in other countries. All grapevine viroid diseases are graft-transmissible and can induce losses especially when associated with viruses. The aim of this work was to confirm infection by Grapevine yellow speckle viroid 1 (GYSVd-1) in grapevine samples exhibiting yellow speckle symptoms in the leaves and in asymptomatic samples sequenced by next generation sequencing (NGS). The occurrence of this viroid in Brazil was further investigated in a second study. Total RNAs and dsRNAs were extracted from five symptomatic plants and 16 asymptomatic samples, respectively. Specific primers were used for RT-PCR and amplified DNA fragments were cloned and sequenced by the Sanger method. Eleven complete nucleotide sequences of GYSVd-1 isolates (366-367 nt) were obtained from NGS and from RT-PCR amplicons. Comparisons showed high identities (95.9-100 %) among ten isolates and an identity of 87.2-90.4 % with a divergent isolate (RM-BR). Phylogenetic analyses placed GYSVd-1 isolates in four clusters (types 1, 2, 3 and 4). All GYSVd-1 infections were confirmed by conventional RT-PCR and RT-qPCR using specific oligonucleotides and a labeled probe. This is the first report and molecular characterization of GYSVd-1 infecting grapevines in Brazil, and our survey indicates that this viroid could be widespread in the major grape producing regions of Brazil.

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“…The SSCP profile approaches allowed us a preliminary selection of isolates to be sequenced, assuming that isolates with similar patterns shared the same sequence (Elleuch, Hamdi, Bessaies, & Fakhfakh, 2013). Based on previous reports, a single strand can form multiple bands one of which being a "conformer", while the sequence is the same (Bodenes, Kremer, & Laigret, 1996;Hayashi, 1991).…”

Section: Iranian Hsvd Population Showed Positive Value Of Tajima's D Andmentioning

confidence: 99%

Genetic diversity of hop stunt viroid from symptomatic and asymptomatic citrus trees in Iran

Vamenani

Rahimian

Alavi

et al. 2019

Journal of Phytopathology

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Hop stunt viroid as the causal agent of cachexia disease has detected from citrus trees in different areas in Iran. Although cachexia has not been reported as a decline disease for citrus trees, it can impair crop quality and reduce plant yields. This study was undertaken to molecularly detect HSVd among different commercial citrus cultivars and determine genetic diversity of this viroid in Mazandaran province of Iran. Sampling was performed from symptomatic and symptomless citrus cultivars in Mazandaran province. HSVd specific primers were used for molecular detection. SSCP and sequencing were applied to assay HSVd genetic diversity. Results showed the detection of HSVd in all symptomatic Satsuma (25 out of 25), Clementine (25 out of 25), sweet lime (20 out of 20) and sweet orange cv. Valencia (7 out of 7), as well as, 31% (14 out of 22), 100% (12 out of 12) and 33% (5 out of 15) of page mandarin, lemon and grapefruit trees, respectively. 10 different HSVd genomes were identified by sequencing the SSCP profiles among which HSVd‐IR1 had the most frequency.

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Single-Strand Conformation Polymorphism for Molecular Variability Studies of Six Viroid Species

Cited by 8 publications

References 23 publications

On the early identification and characterization of pear blister canker viroid, apple dimple fruit viroid, peach latent mosaic viroid and chrysanthemum chlorotic mottle viroid

On the early identification and characterization of pear blister canker viroid, apple dimple fruit viroid, peach latent mosaic viroid and chrysanthemum chlorotic mottle viroid

Detection and molecular characterization of Grapevine yellow speckle viroid 1 isolates infecting grapevines in Brazil

Genetic diversity of hop stunt viroid from symptomatic and asymptomatic citrus trees in Iran

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