Simultaneous detection and genetic variability of stone fruit viroids in the Czech Republic

Hassan, M.; Gómez, Gustavo; Pallás, Vicente; Myrta, A.; Ryšánek, P.

doi:10.1007/s10658-008-9420-0

Cited by 8 publications

(5 citation statements)

References 21 publications

(23 reference statements)

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“…The use of HSVd‐specific probes was crucial for the diagnosis of this pathogen, especially in fruit trees (Astruc et al, 1996). Dot blot and tissue printing hybridization with nonisotopic probes have been used for analysing large numbers of samples and therefore have been very useful for tracking HSVd infection in fruit trees in field conditions (Amari et al, 2001a; Astruc et al, 1996; Cañizares et al, 1998, 1999; Hassan et al, 2009; Mandic et al, 2008). Despite being economical and reliable in optimized conditions, hybridization methods have one important drawback: a limited sensitivity.…”

Section: Survey and Diagnostic Methodsmentioning

confidence: 99%

“…Finally, and based on multiple similarities between viroid replication and trans-acting small interfering RNA tasiRNA processing, it was proposed that the pathogenesis process associated with HSVd infection might be related to the accumulation of vd-sRNAs generated as result from the incorporation of viroid replication intermediates in the tasiRNA biogenesis pathway (Gomez et al, 2009).…”

Section: Pathog Ene S Ismentioning

confidence: 99%

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Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid–host interactions

Marquez‐Molins

Gómez

Pallás

2020

Molecular Plant Pathology

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Taxonomy Hop stunt viroid (HSVd) is the type species of the genus Hostuviroid (family Pospiviroidae). The other species of this genus is Dahlia latent viroid, which presents an identical central conserved region (CCR) but lacks other structural hallmarks present in Hop stunt viroid. HSVd replication occurs in the nucleus through an asymmetric rolling‐circle model as in the other members of the family Pospiviroidae, which also includes the genera Pospiviroid, Cocadviroid, Apscaviroid, and Coleoviroid. Physical properties Hop stunt viroid consists of a single‐stranded, circular RNA of 295–303 nucleotides depending on isolates and sequence variants. The most stable secondary structure is a rod‐like or quasi‐rod‐like conformation with two characteristic domains: a CCR and a terminal conserved hairpin similar to that of cocadviroids. HSVd lacks a terminal conserved region. Hosts and symptoms HSVd infects a very broad range of natural hosts and has been reported to be the causal agent of five different diseases (citrus cachexia, cucumber pale fruit, peach and plum apple apricot distortion, and hop stunt). It is distributed worldwide. Transmission HSVd is transmitted mechanically and by seed.

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Section: Survey and Diagnostic Methodsmentioning

confidence: 99%

Section: Pathog Ene S Ismentioning

confidence: 99%

Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid–host interactions

Marquez‐Molins

Gómez

Pallás

2020

Molecular Plant Pathology

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“…The existing Cycas evolved from the few descendants left by many ancestral groups, so the Cycas are known as "Livingfossil" [10]. The roots, leaves, seeds and trunks of Cycas have different medicinal effects, and leaf extracts have anti-cancer activities [11][12][13]. Therefore, Cycas has important development and utilization value.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Jian¹,

Wang²,

Li³

et al. 2022

Preprint

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Codon use bias is an important characteristic in the process of genetic information transmission of species. With the publication of the genome of C. panzhihuaensis, it is of great significance to investigate the codon use bias for understanding the genetic evolution of this species and for molecular breeding. In this study, Perl language and CodonW 1.4.2 software was used to systematically analyze the coding gene sequences of the C. panzhihuaensis genome, obtain the characteristics of codon use, and identify the sources of variation affecting codon use. The results showed that GC3s content, GCall content, and ENC value were 46.75%, 47.67%, and 52.8 respectively. As the first seed plant, the GC3 content of Cycas is similar to that of most gymnosperms and most dicotyledons, but considerably different from that of monocotyledons.RSCU value was greater than 1, among which 21 codons ended in U or A. Enc-plot analysis, PR2-plot neutral plot analysis, and correlation coefficient analysis of Axis1 with GC3s and CAI revealed that the codon bias was mainly affected by natural selection, but also by mutation pressure and other factors. Thirty-one optimal codons of Cycas genes were screened. This research can provide a reference for the phylogeny and genome codon evolution of Cycas.

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“…Many diagnostic techniques have been developed for plant viroid detection. These include bioassays [1][2][3][4], return-polyacrylamide gel electrophoresis (Return-PAGE) [5], reverse transcriptionpolymerase chain reaction (RT-PCR) [6][7][8][9][10][11][12][13][14][15], RT-PCR using genus degenerate primers and multiplex primers [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30], RT-PCR dot-blot hybridization (RT-PCR-DBH) [31], real time RT-PCR [32][33][34][35][36][37], molecular hybridization [38][39][40], reverse transcription loop-mediated isothermal amplification (RT-LAMP) [41,42] and microarrays [43][44][45][46][47].…”

Section: Introductionmentioning

confidence: 99%

Correction: A Universal Oligonucleotide Microarray with a Minimal Number of Probes for the Detection and Identification of Viroids at the Genus Level

Zhang¹,

Yin²,

Jiang³

et al. 2013

PLoS ONE

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A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.

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Simultaneous detection and genetic variability of stone fruit viroids in the Czech Republic

Cited by 8 publications

References 21 publications

Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid–host interactions

Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid–host interactions

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Correction: A Universal Oligonucleotide Microarray with a Minimal Number of Probes for the Detection and Identification of Viroids at the Genus Level

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