Publications

plus and minus rnas of peach latent mosaic viroid self-cleave in vitro via hammerhead structures.	peach latent mosaic viroid (plmvd), the causal agent of peach latent mosaic disease, has been sequenced and found to be a circular rna molecule of 337 nucleotide residues, which adopts a branched conformation when it is folded in the model of lowest free energy. plmvd exhibits limited homologies with other viroids and some satellite rnas, but it does not have any of the central conserved sequences characteristic of the subgroups of typical viroids. however, a segment of approximately one-third o ...	1992	1373888
identification of a new viroid as the putative causal agent of pear blister canker disease.	a small rna species with the structural and functional properties characteristic of viroids has been isolated from three different pear sources each of which induced symptoms of the pear blister canker (pbc) disease when indexed in the pear indicator a 20. a close association between this rna and pbc disease was established, since two of the three studied sources were known to be affected by this malady only, and the viroid was not detected in healthy pear tissue. moreover, the pbc-associated vi ...	1991	2045786
some properties of the viroid inducing peach latent mosaic disease.	analysis by polyacrylamide gel electrophoresis of nucleic acid extracts from different peach samples, healthy or infected with the peach latent mosaic (plm) disease, demonstrated the association of this disease with an rna exhibiting the electrophoretic properties typical of circular viroid molecules. this rna was called peach latent mosaic viroid (plmv), since a purified preparation of it, when inoculated into gf 305 peach seedlings induced characteristic symptoms of plm disease. plmv was estim ...	1990	2326551
intra- and intermolecular nonenzymatic ligations occur within transcripts derived from the peach latent mosaic viroid.	we report here the nonenzymatic self-ligation of transcripts corresponding to the peach latent mosaic viroid (plmvd). this is the first description of this process with viroid sequences, although it has been reported to occur with human hepatitis delta virus rna. self-ligation occurs when the 5'-hydroxyl and the 2',3'-cyclic phosphate termini produced by the hammerhead self-cleavage of the viroid rna are juxtaposed by the viroid rod-like structure, and a phosphodiester bond is formed between the ...	1995	7571440
the rna of both polarities of the peach latent mosaic viroid self-cleaves in vitro solely by single hammerhead structures.	hammerhead self-cleavage of dimeric, monomeric, truncated and mutated transcripts derived from both polarities of the peach latent mosaic viroid (plmvd) were characterized. in contrast to some results previously published for a very close sequence variant (see ref. 1), these rnas exhibit a virtually identical self-cleavage during transcription and after purification. by self-cleavage of dimeric transcripts with normal and mutated hammerhead domains and by complementation experiments, we show tha ...	1995	7708488
evidence for a model ancestral viroid.	the generation of a phylogenetic tree of viroids and viroid-like plant satellite rnas via computer analysis, coupled with several conspicuous biochemical characteristics of the rolling circle replication of these rnas -including both self-cleavage and self-ligation- leads us to propose the peach latent mosaic viroid (plmvd) as a current "living fossil" dating from a precellular world. incorporated within this proposal is a revised mechanism of plmvd rolling circle replication which requires a mi ...	1995	8643352
chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes.	the causal agent of chrysanthemum chlorotic mottle (cchm) disease has been identified, cloned, and sequenced. it is a viroid rna (cchmvd) of 398-399 nucleotides. in vitro transcripts with the complete cchmvd sequence were infectious and induced the typical symptoms of the cchm disease. cchmvd can form hammerhead structures in both polarity strands. plus and minus monomeric cchmvd rnas self-cleaved during in vitro transcription and after purification as predicted by these structures, which are st ...	1997	9326597
peach latent mosaic viroid is locked by a 2',5'-phosphodiester bond produced by in vitro self-ligation.	although some viroid-like satellite rnas possess self-cleavage and self-ligation activities, we show that the peach latent mosaic viroid (plmvd) is unique among all known viroids since it also has such activities. these catalytic activities should have important roles in the rolling circle replication of plmvd. according to this proposed mechanism, self-cleavage of the multimeric strands occurs via hammerhead structures producing monomers possessing 2',3'-cyclic phosphate and 5'-hydroxyl termini ...	1997	9356244
in vitro and in vivo self-cleavage of a viroid rna with a mutation in the hammerhead catalytic pocket.	peach latent mosaic viroid (plmvd) can adopt hammerhead structures in both polarity strands. in the course of a study on the variability of this viroid a natural sequence variant has been characterized in which the hammerhead structure of the plus polarity strand has the sequence ccga instead of the conserved uridine turn motif cuga present in the catalytic pocket of all natural hammerhead structures. the viroid rna containing this mutant hammerhead structure, but not those with the two other po ...	1998	9518479
a small-scale procedure for extracting nucleic acids from woody plants infected with various phytopathogens for pcr assay.	the complexity of most nucleic acid extraction procedures limits the number of samples that can be easily processed for analysis by polymerase chain reaction (pcr). a simple, small-scale procedure was developed which can be carried out entirely in 1.5-ml microfuge tubes whereby the container and contents are frozen with liquid nitrogen, tissue is pulverized, and targeted nucleic acids are extracted. dna of bacterial and phytoplasmal plant pathogens was extracted in hot ctab buffer followed by ch ...	1998	9628220
specific rna self-cleavage in coconut cadang cadang viroid: potential for a role in rolling circle replication.	the rolling circle replication of the small, single-stranded viroid rnas requires a specific processing reaction to produce monomeric rnas that are ligated into the final circular form. for avocado sunblotch viroid, peach latent mosaic viroid, and chrysanthemum chlorotic mottle viroid, the hammerhead self-cleavage reaction is considered to provide this processing reaction. we have searched for a similar type of reaction in the 246-nt coconut cadang cadang viroid, the smallest viroid of the 24-me ...	1998	9630248
genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasispecies.	the peach latent mosaic viroid (plmvd) is used to study the interactions between a viroid containing hammerhead ribozymes and its natural host, peach. to gain insight into the molecular basis of the phenotypic effects observed upon viroid infection, sequence variants from three plmvd isolates that differ in symptom expression on the peach indicator gf-305 have been characterized. analysis of the primary structures of a total of 29 different sequence variants derived from a severe and two latent ...	1998	9696836
subcellular localization and rolling circle replication of peach latent mosaic viroid: hallmarks of group a viroids.	we characterized the peach latent mosaic viroid (plmvd) replication intermediates that accumulate in infected peach leaves and determined the tissue and subcellular localization of the rna species. using in situ hybridization, we showed that plmvd strands of both plus and minus polarities concentrate in the cells forming the palisade parenchyma. at the cellular level, plmvd was found to accumulate predominantly in chloroplasts. northern blot analyses demonstrated that plmvd replicates via a symm ...	1999	10400727
rapid generation of genetic heterogeneity in progenies from individual cdna clones of peach latent mosaic viroid in its natural host.	viroids, small single-stranded circular rnas endowed with autonomous replication, are unique systems to conduct evolutionary studies of complete rna genomes. the primary structure of 36 progeny variants of peach latent mosaic viroid (plmvd), evolved from inoculations of the peach indicator gf-305 with four individual plmvd cdnas differing in their pathogenicity, has been determined. most progeny variants had unique sequences, revealing that the extremely heterogeneous character of plmvd natural ...	1999	10466824
sensitive detection of potato spindle tuber and temperate fruit tree viroids by reverse transcription-polymerase chain reaction-probe capture hybridization.	a rapid and sensitive assay for the specific detection of plant viroids using reverse transcription-polymerase chain reaction (rt-pcr) -probe capture hybridization (rt-pcr-enzyme-linked immunosorbent assay (elisa)) was developed. the assay was applied successfully for the detection of potato spindle tuber viroid, peach latent mosaic viroid, or apple scar skin viroid from viroid infected leaf tissue. clarified sap extract from infected leaf tissue was treated first with genereleaser polymeric mat ...	1999	10471024
mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure.	we have investigated the secondary structure of peach latent mosaic viroid (plmvd) in solution, and we present here the first description of the structure of a branched viroid in solution. different plmvd transcripts of plus polarity were produced by using the circularly permuted rna method and the exploitation of rna internal secondary structure to position the 5' and 3' termini and studied by nuclease mapping and binding shift assays using dna and rna oligonucleotides. we show that plmvd folds ...	2000	10684279
sequencing of peach latent mosaic viroid variants from nine north american peach cultivars shows that this rna folds into a complex secondary structure.	we sequenced 34 new peach latent mosaic viroid (plmvd) variants isolated from nine different peach cultivars. this study provides the widest view of plmvd diversity reported to date and includes the original characterization of north american variants, which cannot be differentiated from european sequences. plmvd appears as a species in which each isolate is a complex mixture of rnas. analysis of base-pair covariations supports the hypothesis that plmvd folds into a complex branched structure wi ...	2000	10814568
natural 2',5'-phosphodiester bonds found at the ligation sites of peach latent mosaic viroid.	peach latent mosaic viroid (plmvd) is a circular rna pathogen that replicates in a dna-independent fashion via a rolling circle mechanism. plmvd has been shown to self-ligate in vitro primarily via the formation of 2',5'-phosphodiester bonds; however, in vivo the occurrence and necessity of this nonenzymatic mechanism are not evident. here, we unequivocally report the presence of 2', 5'-phosphodiester bonds at the ligation site of circular plmvd strands isolated from infected peach leaves. these ...	2001	11119569
study of the polymerization step of the rolling circle replication of peach latent mosaic viroid.	we have developed an in vitro transcriptional assay using escherichia coli rna polymerase to initiate the replication of peach latent mosaic viroid (plmvd). regardless of the polarity of the plmvd strand used as template, initiation in vitro occurred at the same hairpin structure. these initiation sites correspond to the 5'-ends of two small (280 nt) plmvd-related rnas found in infected peach leaves. using a series of truncated plmvd-derived transcripts, we have demonstrated that the viroid doma ...	2001	11699960
characterization of a viroid-derived rna promoter for the dna-dependent rna polymerase from escherichia coli.	this paper attributes a novel function, namely, that of transcriptional promoter, to the self-complementary, self-cleaving hammerhead rna sequences found in rna derived from the peach latent mosaic viroid (plmvd). the features of this rna promoter, which adopts a hairpin structure that can be utilized by escherichia coli rna polymerase (rnap) for in vitro transcription, that trigger the rnap driven transcription and are responsible for the specific initiation of synthesis are described. the esse ...	2002	12009921
a novel multiplex rt-pcr probe capture hybridization (rt-pcr-elisa) for simultaneous detection of six viroids in four genera: apscaviroid, hostuviroid, pelamoviroid, and pospiviroid.	a rapid and sensitive assay was developed for the detection and identification of viroids by standard or multiplex reverse transcription-polymerase chain reaction (rt-pcr)-probe capture hybridization (rt-pcr-elisa). the assay was applied successfully for the detection and identification of the following six viroid species from infected tissues: potato spindle tuber viroid (pospiviroid), peach latent mosaic viroid (pelamoviroid), apple scar skin viroid (apscaviroid), apple dimple fruit viroid (ap ...	2002	12176148
peach latent mosaic viroid variants inducing peach calico (extreme chlorosis) contain a characteristic insertion that is responsible for this symptomatology.	the involvement of peach latent mosaic viroid (plmvd) in an extensive chlorosis of peach known as calico (pc) has been advanced but ultimate proof is lacking. sequencing of 16 full-length plmvd cdna clones of a pc isolate revealed two groups of variants. nine had a size (336-338 nt) similar to that of typical plmvd variants of nonsymptomatic and mosaic-inducing isolates, whereas the other 7 were longer (348-351 nt) due to an insertion of 12-13 nt. this insertion was always found in the hairpin l ...	2003	12954216
development of a one tube-one step rt-pcr protocol for the detection of seven viroids in four genera: apscaviroid, hostuviroid, pelamoviroid and pospiviroid.	a one tube-one step rt-pcr was developed for the detection of seven viroids (apple scar skin viroid, apple dimple fruit viroid, pear blister canker viroid, hop stunt viroid, chrysanthemum stunt viroid, citrus exocortis viroid and peach latent mosaic viroid) in four genera that infect eight plant species. the efficiency and specificity of this method were optimized by the use of moloney-murine leukemia virus (m-mlv) reverse-transcriptase and hotstartaq dna polymerase which allowed increase sensit ...	2004	15350729
comparative single-turnover kinetic analyses of trans-cleaving hammerhead ribozymes with naturally derived non-conserved sequence motifs.	trans-cleaving hammerhead ribozyme variants were generated with mimicked non-conserved internal loop motifs derived from five structurally diverse natural cis-cleaving ribozymes. most modified trans-cleaving variants showed enhanced single-turnover cleavage rates relative to minimal counterparts that lack tertiary interactions between internal loop motifs i and ii, and relative to controls with sequence changes in loop i. the trans-cleaving ribozyme derived from the positive strand of peach late ...	2005	15757651
identification of a peach latent mosaic viroid hairpin able to act as a dicer-like substrate.	the ability of several viroids to induce posttranscriptional gene silencing has been demonstrated; however, the structure recognized by the dicer enzyme(s) responsible for the initiation of this mechanism remains a mystery. here, we show that the hairpin known to be implicated in the replication of peach latent mosaic viroid has the ability to trigger the dicer enzyme(s). this domain, which is composed of a succession of several small stems separated by symmetrical bulges, is reminiscent of the ...	2005	15858039
a kissing-loop interaction in a hammerhead viroid rna critical for its in vitro folding and in vivo viability.	chrysanthemum chlorotic mottle viroid (cchmvd) rna (398-401 nucleotides) can form hammerhead ribozymes that play a functional role in its replication through a rolling-circle mechanism. in contrast to most other viroids, which adopt rod-like or quasi-rod-like secondary structures of minimal free energy, the computer-predicted conformations of cchmvd and peach latent mosaic viroid (plmvd) rnas are branched. moreover, the covariations found in a number of natural cchmvd variants support that the s ...	2005	15928342
a short double-stranded rna motif of peach latent mosaic viroid contains the initiation and the self-cleavage sites of both polarity strands.	the transcription initiation sites of viroid rnas, despite their relevance for replication and in vivo folding, are poorly characterized. here we have examined this question for peach latent mosaic viroid (plmvd), which belongs to the family of chloroplastic viroids with hammerhead ribozymes (avsunviroidae), by adapting an rna ligase-mediated rapid amplification of cdna ends methodology developed for mapping the genuine capped 5' termini of eukaryotic messenger rnas. to this aim, the characteris ...	2005	16188995
variants of peach latent mosaic viroid inducing peach calico: uneven distribution in infected plants and requirements of the insertion containing the pathogenicity determinant.	previous characterization of peach latent mosaic viroid (plmvd) variants from a single peach calico (pc) isolate showed that pc symptoms are induced by variants with a 12-13 nt insertion at a specific position and folding into a hairpin with a u-rich loop. here, this study was extended to two other pc isolates. plmvd variants with insertions similar to those reported previously (type 1), predominated in one isolate (pc-p2). the second (pc-p1), in addition to these variants, contained others with ...	2006	16361436
detection and epidemiological characteristics of peach latent mosaic viroid in tunisia.	a rapid and sensitive assay was developed for the detection and identification of peach latent mosaic viroid (plmvd) by reverse transcription-polymerase chain reaction (rt-pcr) in infected tissues from tunisian orchards. the test was initially performed by using total rna preparations from selected isolates and then applied on total rna preparations from leaf or bark tissues of fruit trees collected in 2003 in 20 orchards in the north of tunisia and the sahel. plmvd occurred in peach and pear tr ...	2005	16637166
improving the sensitivity of single-strand conformation polymorphism (sscp) to study the variability of plmvd.	single-strand conformation polymorphism (sscp) was used to characterize viroids. eight cdna clones, which showed identical profiles in preliminary existing sscp analysis but had different sequences, were chosen to develop a sensitive sscp technique for identifying the variability of peach latent mosaic viroid (plmvd). polyacrylamide gel electrophoresis (page) conditions were optimized to improve the sensitivity of the existing sscp, and a modified sscp protocol was developed. the results indicat ...	2006	16644025
an element of the tertiary structure of peach latent mosaic viroid rna revealed by uv irradiation.	following uv irradiation, denaturing polyacrylamide gel electrophoresis and northern blot hybridization revealed a cross-link in peach latent mosaic viroid (plmvd) plus-strand rna. primer extension and partial alkaline hydrolysis of the uv-irradiated plmvd plus-strand rna resulting from the hammerhead-mediated self-cleavage mapped the cross-link at u81 and at the 3'-terminal c289 (or at a very proximal nucleotide). supporting this notion, in vitro-synthesized plmvd plus-strand rnas with short in ...	2006	16940546
molecular features of new peach latent mosaic viroid variants suggest that recombination may have contributed to the evolution of this infectious rna.	nucleotide sequences of a broad range of peach latent mosaic viroid (plmvd) variants were determined. the variants were isolated from peach, pear, and almond tree samples collected in tunisia. sequence analysis confirmed the high variability of plmvd, as no less than 119 new variants were identified. variations included new polymorphic positions, insertions of 11 to 14 nucleotides, and new mutations within the hammerhead self-cleavage motifs. we provide the first covariation-based evidence for c ...	2007	17113618
genomic structure of new tunisian peach latent mosaic viroid variants.	peach latent mosaic viroid (plmvd) is a single-stranded circular rna that do not code for proteins and ranges in size from 335 to 351 nucleotides. it mainly infects peach. in this study, the sequence of 20 complete cdna clones derived from seven plmvd isolates detected in five tunisian peach cultivars was analysed in 3 steps: primary structure, phylogeny and secondary structure. the analysis of the primary structure revealed that all the 20 cdna clones sequences corresponded to different variant ...	2006	17390888
idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof.	the hammerhead ribozyme is a small rna endonuclease found in sub-viral plant pathogens, in transcripts from certain animal satellite dnas and encoded at distinct loci of arabidopsis thaliana. kinetic analyses of tertiary stabilised ribozymes from peach latent mosaic viroid (plmvd), schistosoma mansoni and a. thaliana revealed a ten-fold difference in cleavage rates. core nucleotide variations affected cleavage reactions least in the a. thaliana ribozyme, and most in the s. mansoni ribozyme. the ...	2007	17570826
the tolerance to exchanges of the watson crick base pair in the hammerhead ribozyme core is determined by surrounding elements.	tertiary interacting elements are important features of functional rna molecules, for example, in all small nucleolytic ribozymes. the recent crystal structure of a tertiary stabilized type i hammerhead ribozyme revealed a conventional watson-crick base pair in the catalytic core, formed between nucleotides c3 and g8. we show that any watson-crick base pair between these positions retains cleavage competence in two type iii ribozymes. in the arabidopsis thaliana sequence, only moderate differenc ...	2007	17666711
a viroid rna with a specific structural motif inhibits chloroplast development.	peach latent mosaic viroid (plmvd) is a chloroplast-replicating rna that propagates in its natural host, peach (prunus persica), as a complex mixture of variants, some of which are endowed with specific structural and pathogenic properties. this is the case of variant pc-c40, with an insertion of 12 to 13 nucleotides that folds into a hairpin capped by a u-rich loop, which is responsible for an albino-variegated phenotype known as peach calico (pc). we have applied a combination of ultrastructur ...	2007	18055612
the peach latent mosaic viroid replication initiation site is located at a universal position that appears to be defined by a conserved sequence.	viroids replicate through a rolling circle mechanism that is exclusively rna dependent. in this study, we initially revisited the determination of the replication initiation sites of peach latent mosaic viroid (plmvd). a universal initiation site for each of the plmvd polarities (position a50/c51 and u284 for the plus and minus strands, respectively) that is shared by a relatively wide repertoire of viroid variants was identified, in agreement with a previous report based on a different methodol ...	2008	18190946
characterization of the sirnas associated with peach latent mosaic viroid infection.	the peach latent mosaic viroid (plmvd) is a small, circular rna species that has been shown to induce rna silencing in plants. with the goal of better understanding the biological mechanism underlying this process, the sirnas found in plmvd infected peach leaves were isolated and sequenced. analysis of the resulting data prompted several conclusions, including: i. plmvd strands of both polarities are substrates for the dicer-like enzymes found in peach leaves; ii. the more highly structured regi ...	2009	19068263
sensitive and rapid detection of peach latent mosaic viroid by the reverse transcription loop-mediated isothermal amplification.	a reverse transcription loop-mediated isothermal amplification (rt-lamp) method for the detection of peach latent mosaic viroid (plmvd) was developed. four primer sets (old, old1, new, and fukuta's) were designed originally. based on initial experiments the set old1 was selected for further evaluation. simple and accelerated rt-lamp was preformed using degenerate and no degenerate forward-loop (f-loop) and backward-loop (b-loop) primers. degenerate primers were selected, and after determination ...	2009	19409419
probe binding to host proteins: a cause for false positive signals in viroid detection by tissue hybridization.	molecular hybridization assay, especially involving the use of tissues directly, has been developed as a rapid, simple and important technique for plant pathogen detection and/or gene expression analysis on a large scale. in theory, this method relies on the specific binding of a labeled probe to a target nucleotide sequence. however, occasional false positive reactions can pose a problem in its application and the cause is often not well understood. here, we show that in tissue-printing hybridi ...	2009	19540886
identification of proteins from prunus persica that interact with peach latent mosaic viroid.	peach latent mosaic viroid (plmvd) is a small, single-stranded, circular rna pathogen that infects prunus persica trees. as with all other known viroids, the plmvd genome does not encode any proteins. consequently, it must interact with host cellular factors in order to ensure its life cycle. with the objective of identifying cellular proteins that interact with plmvd, northwestern hybridizations were performed using partially purified peach leaf extracts. mass spectrometric analysis of the dete ...	2009	19759139
deep sequencing of the small rnas derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis.	northern-blot hybridization and low-scale sequencing have revealed that plants infected by viroids, non-protein-coding rna replicons, accumulate 21-24 nt viroid-derived small rnas (vd-srnas) similar to the small interfering rnas, the hallmarks of rna silencing. these results strongly support that viroids are elicitors and targets of the rna silencing machinery of their hosts. low-scale sequencing, however, retrieves partial datasets and may lead to biased interpretations. to overcome this restra ...	2009	19847296
the rna strands of the plus and minus polarities of peach latent mosaic viroid fold into different structures.	it is believed that peach latent mosaic viroid (plmvd) strands of both the plus and minus polarities fold into similar secondary and tertiary structures. in order to verify this hypothesis, the behavior of both strands in three biophysical assays was examined. plmvd transcripts of plus and minus polarity were found to exhibit distinct electrophoretic mobility properties under native conditions, to precipitate differently in the presence of lithium chloride, and to possess variable thermal denatu ...	2010	20089682
in-depth sequencing of the sirnas associated with peach latent mosaic viroid infection.	it has been observed that following viroid infection, there is an accumulation of viroid-derived sirnas in infected plants. some experimental results suggest that these small rnas may be produced by the plant defense system to protect it from infection, indicating that viroids can elicit the rna-silencing pathways. the objective of this study is to identify in the peach latent mosaic viroid (plmvd), a model rna genome, the regions that are most susceptible to rna interference machinery.	2010	20158907
peach latent mosaic viroid: not so latent.	summary taxonomy: peach latent mosaic viroid (plmvd) is the type species of the genus pelamoviroid within the family avsunviroidae of chloroplastic viroids with hammerhead ribozymes. physical properties: a small circular rna of 336-351 nt (differences in size result from the absence or presence of certain insertions) adopting a branched conformation stabilized by a pseudoknot between two kissing loops. this particular conformation is most likely responsible for the insolubility of plmvd in highl ...	2006	20507441
trans-cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid rna.	trans-cleaving hammerheads with discontinuous or extended stem i and with tertiary stabilizing motifs (tsms) have been tested previously against short rna substrates in vitro at low mg(2+) concentration. however, the potential of these ribozymes for targeting longer and structured rnas in vitro and in vivo has not been examined. here, we report the in vitro cleavage of short rnas and of a 464-nt highly structured rna from potato spindle tuber viroid (pstvd) by hammerheads with discontinuous and ...	2010	21097888
mapping studies of the peach latent mosaic viroid reveal novel structural features.	knowledge of the structure of a viroid is critically important to elucidate the roles played by the various rna motifs in the steps of the viroid's life cycle. a new technique, rna-selective 2'-hydroxyl acylation analysed by primer extension (shape), has recently been shown to be fast, reliable and applicable to the study of various rna molecules. consequently, this method was used to probe sequence variants of peach latent mosaic viroid (plmvd). initially, probing data from rna strands of both ...	2011	21726370
new iranian and australian peach latent mosaic viroid variants and evidence for rapid sequence evolution.	peach latent mosaic viroid isolates from peach and plum in iran have been compared with an australian isolate from nectarine. thirteen sequence variants 336-338 nt in size were obtained. all variants clustered phylogenetically with variants reported from several hosts and countries. a total nucleic acid extract, a slightly longer than full-length rt-pcr amplicon, and a recombinant plasmid clone from the australian isolate were all infectious to, and symptomatic in, mechanically inoculated peach ...	2011	22075917
small rnas containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mrna as predicted by rna silencing.	how viroids, tiny non-protein-coding rnas (~250-400 nt), incite disease is unclear. one hypothesis is that viroid-derived small rnas (vd-srnas; 21-24 nt) resulting from the host defensive response, via rna silencing, may target for cleavage cell mrnas and trigger a signal cascade, eventually leading to symptoms. peach latent mosaic viroid (plmvd), a chloroplast-replicating viroid, is particularly appropriate to tackle this question because it induces an albinism (peach calico, pc) strictly assoc ...	2012	22332758
involvement of the chloroplastic isoform of trna ligase in the replication of viroids belonging to the family avsunviroidae.	avocado sunblotch viroid, peach latent mosaic viroid, chrysanthemum chlorotic mottle viroid, and eggplant latent viroid (elvd), the four recognized members of the family avsunviroidae, replicate through the symmetric pathway of an rna-to-rna rolling-circle mechanism in chloroplasts of infected cells. viroid oligomeric transcripts of both polarities contain embedded hammerhead ribozymes that, during replication, mediate their self-cleavage to monomeric-length rnas with 5'-hydroxyl and 2',3'-phosp ...	2012	22623792
ancient rna? rt-pcr of 50-year-old rna identifies peach latent mosaic viroid.	the preservation of macromolecules is at best haphazard. modern techniques have improved the detection of ancient dna and proteins, but there is little information on the preservation of rna. fifty-year-old dried leaf material showing symptoms of peach calico disease was used successfully in rt-pcrs to amplify peach latent mosaic viroid (plmvd) rna and the mrna for the large subunit of ribulose 1,5-bisphosphate carboxylase (rubisco). these results indicate that naked rna may be preserved, under ...	2013	23138153
a remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid.	microarray profiling is a powerful technique to investigate expression changes of large amounts of genes in response to specific environmental conditions. the majority of the studies investigating gene expression changes in virus-infected plants are limited to interactions between a virus and a model host plant, which usually is arabidopsis thaliana or nicotiana benthamiana. in the present work, we performed microarray profiling to explore changes in the expression profile of field-grown prunus ...	2013	23710752
virulence determination and molecular features of peach latent mosaic viroid isolates derived from phenotypically different peach leaves: a nucleotide polymorphism in l11 contributes to symptom alteration.	symptoms of chlorosis along leaf edges (chlorosis-edge), along leaf veins (chlorosis-vein) and yellowing on peach leaves have been observed for a long history in the field, while the pathological factor(s) responsible for these symptoms remained unknown. peach latent mosaic viroid (plmvd) was detected in the leaves collected from three unique phenotypic peach trees showing above mentioned symptoms. the obtained plmvd isolates were subjected to population structure analyses and biological assays ...	2013	23973915
deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity.	viroids are small circular single-stranded infectious rnas characterized by a relatively high mutation level. knowledge of their sequence heterogeneity remains largely elusive and previous studies, using sanger sequencing, were based on a limited number of sequences. in an attempt to address sequence heterogeneity from a population dynamics perspective, a gf305-indicator peach tree was infected with a single variant of the avsunviroidae family member peach latent mosaic viroid (plmvd). six month ...	2014	24498066
complete genome sequences of peach latent mosaic viroid from a single peach cultivar.	peach latent mosaic viroid (plmvd) is a member of the genus pelamoviroid in the family avsunviroidae and infects peach trees. we de novo assembled a plmvd genome from a peach transcriptome and identified 18 variants in a single peach cultivar, after sequencing 20 plmvd genomes by sanger sequencing.	2015	26404583
interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection.	natural populations of peach latent mosaic viroid (plmvd) are complex mixtures of variants. during routine testing, taqman rtrt-pcr and rna gel-blot hybridization produced discordant results with some plmvd isolates. analysis of the corresponding populations showed that they were exclusively composed of variants (of class ii) with a structural domain different from that of the reference and many other variants (of class i) targeted by the taqman rtrt-pcr probe. bioassays in peach revealed that a ...	2017	28211491