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Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection

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Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection

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dc.contributor.author Serra Alfonso, Pedro es_ES
dc.contributor.author Bertolini, Edson es_ES
dc.contributor.author Martinez, M. Carmen es_ES
dc.contributor.author Cambra, Mariano es_ES
dc.contributor.author Flores Pedauye, Ricardo es_ES
dc.date.accessioned 2018-07-26T07:05:36Z
dc.date.available 2018-07-26T07:05:36Z
dc.date.issued 2017 es_ES
dc.identifier.issn 2045-2322 es_ES
dc.identifier.uri http://hdl.handle.net/10251/106294
dc.description.abstract [EN] 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 representative PLMVd variant of class II replicated without symptoms, generated a progeny with low nucleotide diversity, and, intriguingly, outcompeted a representative symptomatic variant of class I when co-inoculated in equimolecular amounts. A number of informative positions associated with the higher fitness of variants of class II have been identified, and novel sets of primers and probes for universal or specific TaqMan rtRT-PCR detection of PLMVd variants have been designed and tested. es_ES
dc.description.sponsorship We thank A. Ahuir for excellent technical assistance and Dr. Francesco Di Serio for suggestions. This work was supported by grant BFU2014-56812-P (to R.F.) from Ministerio de Economia y Competitividad (MINECO) of Spain. P.S. was the recipient of a postdoctoral contract from MINECO and E. Bertolini of an INIA-CCA2011-2016 contract also from MINECO. es_ES
dc.language Inglés es_ES
dc.publisher Nature Publishing Group es_ES
dc.relation.ispartof Scientific Reports es_ES
dc.rights Reconocimiento (by) es_ES
dc.title Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1038/srep42825 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//BFU2014-56812-P/ES/VIROIDES, LOS PARASITOS EXTREMOS: EVOLUCION ESPACIO-TEMPORAL, PATOGENESIS MEDIADA POR SILENCIAMIENTO VIA RNA, Y DEGRADACION/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//INIA-CCA2011-2016
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes es_ES
dc.description.bibliographicCitation Serra Alfonso, P.; Bertolini, E.; Martinez, MC.; Cambra, M.; Flores Pedauye, R. (2017). Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection. Scientific Reports. 7. https://doi.org/10.1038/srep42825 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1038/srep42825 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 7 es_ES
dc.identifier.pmid 28211491 en_EN
dc.identifier.pmcid PMC5314366 en_EN
dc.relation.pasarela S\357393 es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.description.references Diener, T. O. Discovering viroids - a personal perspective. Nat. Rev. Microbiol. 1, 75–80 (2003). es_ES
dc.description.references Flores, R., Hernández, C., Martínez de Alba, A. E., Daròs, J. A. & Di Serio, F. Viroids and viroid–host interactions. Annu. Rev. Phytopathol. 43, 117–139 (2005). es_ES
dc.description.references Tsagris, E. M., Martínez de Alba, A. E., Gozmanova, M. & Kalantidis, K. Viroids. Cell Microbiol. 10, 2168–2179 (2008). es_ES
dc.description.references Ding, B. The biology of viroid–host interactions. Annu. Rev. Phytopathol. 47, 105–131 (2009). es_ES
dc.description.references Kovalskaya, N. & Hammond, R. W. Molecular biology of viroid-host interactions and disease control strategies. Plant Sci. 228, 48–60 (2014). es_ES
dc.description.references Palukaitis, P. What has been happening with viroids? Virus Genes 49, 175–184 (2014). es_ES
dc.description.references Flores, R. et al. Viroids, the simplest RNA replicons: how they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Res. 209, 136–145 (2015). es_ES
dc.description.references Hernández, C. & Flores, R. Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. Proc. Natl. Acad. Sci. USA 89, 3711–3715 (1992). es_ES
dc.description.references Flores, R. et al. Peach latent mosaic viroid: not so latent. Mol. Plant Pathol. 4, 209–221 (2006). es_ES
dc.description.references Ambrós, S., Hernández, C., Desvignes, J. C. & Flores, R. Genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasi-species. J. Virol. 72, 7397–7406 (1998). es_ES
dc.description.references Ambrós, S., Hernández, C. & Flores, R. Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host. J. Gen. Virol. 80, 2239–2252 (1999). es_ES
dc.description.references Malfitano, M. et al. Peach latent mosaic viroid variants inducing peach calico contain a characteristic insertion that is responsible for this symptomatology. Virology 313, 492–501 (2003). es_ES
dc.description.references Rodio, M. E., Delgado, S., Flores, R. & Di Serio, F. Variants of peach latent mosaic viroid inducing peach calico: uneven distribution in infected plants and requirements of the insertion containing the pathogenicity determinant. J. Gen. Virol. 87, 231–240 (2006). es_ES
dc.description.references Rodio, M. E. et al. A viroid RNA with a specific structural motif inhibits chloroplast development. Plant Cell 19, 3610–3626 (2007). es_ES
dc.description.references Navarro, B. et al. Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. Plant J. 70, 991–1003 (2012). es_ES
dc.description.references Yazarlou, A., Jafarpour, B., Tarighi, S., Habili, N. & Randles, J. W. New Iranian and Australian peach latent mosaic viroid variants and evidence for rapid sequence evolution. Arch. Virol. 157, 343–347 (2012). es_ES
dc.description.references Wang, L. P. et al. 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. Virus Res. 177, 171–178 (2013). es_ES
dc.description.references Desvignes, J. C. The virus diseases detected in greenhouse and in the field by the peach seedling GF 305 indicator. Acta Hortic. 67, 315–323 (1976). es_ES
dc.description.references Flores, R. & Llácer, G. Isolation of a viroid-like RNA associated with peach latent mosaic disease. Acta Hortic. 235, 325–332 (1988). es_ES
dc.description.references Flores, R., Hernández, C., Desvignes, J. C. & Llácer, G. Some properties of the viroid inducing the peach latent mosaic disease. Res. Virol. 141, 109–118 (1990). es_ES
dc.description.references Ambrós, S., Desvignes, J. C., Llácer, G. & Flores, R. Peach latent mosaic and pear blister canker viroids: detection by molecular hybridization and relationships with specific maladies affecting peach and pear trees. Acta Hortic. 386, 515–521 (1995). es_ES
dc.description.references Loreti, S., Faggioli, F. & Barba, M. A rapid extraction method to detect peach latent mosaic viroid by molecular hybridization. Acta Hortic. 386, 560–564 (1995). es_ES
dc.description.references Skrzeczkowski, L. J., Howell, W. E. & Mink, G. I. Occurrence of peach latent mosaic viroid in commercial peach and nectarine cultivars in the US. Plant Dis. 80, 823 (1996). es_ES
dc.description.references Hadidi, A., Giunchedi, L., Shamloul, A. M., Poggi-Pollini, C. & Amer, M. A. Occurrence of peach latent mosaic viroid in stone fruits and its transmission with contaminated blades. Plant Dis. 81, 154–158 (1997). es_ES
dc.description.references Xu, W. X. et al. Probe binding to host proteins: a cause for false positive signals in viroid detection by tissue hybridization. Virus Res. 145, 26–30 (2009). es_ES
dc.description.references Shamloul, A. M. et al. Peach latent mosaic viroid: nucleotide sequence of an Italian isolate, sensitive detection using RT-PCR and geographic distribution. Acta Hortic. 386, 522–530 (1995). es_ES
dc.description.references Shamloul, A. M. & Hadidi, A. Sensitive detection of potato spindle tuber and temperate fruit tree viroids by reverse transcription-polymerase chain reaction-probe capture hybridization. J. Virol. Methods 80, 145–155 (1999). es_ES
dc.description.references Shamloul, A. M., Faggioli, F., Keith, J. M. & Hadidi, A. 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 . J. Virol. Methods 105, 115–121 (2002). es_ES
dc.description.references Ragozzino, E., Faggioli, F. & Barba, M. Development of a one tube-one step RT-PCR protocol for the detection of seven viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid and Pospiviroid. J. Virol. Methods 121, 25–29 (2004). es_ES
dc.description.references Luigi, M. & Faggioli, F. Development of quantitative real-time RT-PCR for the detection and quantification of peach latent mosaic viroid. Eur. J. Plant Pathol. 130, 109–116 (2011). es_ES
dc.description.references Parisi, O., Lepoivre, P. & Jijakli, M. H. Development of a quick quantitative real-time PCR for the in vivo detection and quantification of peach latent mosaic viroid. Plant Dis. 95, 137–142 (2011). es_ES
dc.description.references Lin, L., Li, R., Bateman, M., Mock, R. & Kinard, G. Development of a multiplex TaqMan real-time RT-PCR assay for simultaneous detection of Asian prunus viruses, plum bark necrosis stem pitting associated virus, and peach latent mosaic viroid. Eur. J. Plant Pathol. 137, 797–804 (2013). es_ES
dc.description.references Zhang, Y. J. et al. A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level. PLoS One 8, e64474 (2013). es_ES
dc.description.references Di Serio, F. et al. Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLoS One 4, e7539 (2009). es_ES
dc.description.references Bolduc, F., Hoareau, C., St-Pierre, P. & Perreault, J. P. In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMC Mol. Biol. 11, 16 (2010). es_ES
dc.description.references Glouzon, J. P. S., Bolduc, F., Wang, S., Najmanovich, R. J. & Perreault, J. P. Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity. PLoS One 9, e87297 (2014). es_ES
dc.description.references Jo, Y. et al. Complete genome sequences of peach latent mosaic viroid from a single peach cultivar. Genome Announc. 3, e01098–15 (2015). es_ES
dc.description.references Pelchat, M. et al. Sequencing of peach latent mosaic viroid variants from nine North American peach cultivars shows that this RNA folds into a complex secondary structure. Virology 271, 37–45 (2000). es_ES
dc.description.references Bussière, F., Ouellet, J., Côté, F., Lévesque, D. & Perreault, J. P. Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure. J. Virol. 74, 2647–2654 (2000). es_ES
dc.description.references Dubé, A., Baumstark, T., Bisaillon, M. & Perreault, J. P. The RNA strands of the plus and minus polarities of peach latent mosaic viroid fold into different structures. RNA 16, 463–473 (2010). es_ES
dc.description.references Dubé, A., Bolduc, F., Bisaillon, M. & Perreault, J. P. Mapping studies of the peach latent mosaic viroid reveal novel structural features. Mol. Plant Pathol. 12, 688–701 (2011). es_ES
dc.description.references Gago, S., De la Peña, M. & Flores, R. A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability. RNA 11, 1073–1083 (2005). es_ES
dc.description.references Olmos, A., Bertolini, E., Gil, M. & Cambra, M. Real-time assay for quantitative detection of non-persistently transmitted plum pox virus RNA targets in single aphids. J. Virol. Methods 128, 151–155 (2005). es_ES
dc.description.references Ruffner, D. E., Stormo, G. D. & Uhlenbeck, O. C. Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29, 10695–10702 (1990). es_ES
dc.description.references Symons, R. H. Plant pathogenic RNAs and RNA catalysis. Nucleic Acids Res. 25, 2683–2689 (1997). es_ES
dc.description.references Flores, R., Hernández, C., De la Peña, M., Vera, A. & Daròs, J. A. Hammerhead ribozyme structure and function in plant RNA replication. Meth. Enzymol. 341, 540–552 (2001). es_ES
dc.description.references Hutchins, C., Rathjen, P. D., Forster, A. C. & Symons, R. H. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res. 14, 3627–3640 (1986). es_ES
dc.description.references Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R. & Bruening, G. Autolytic processing of dimeric plant virus satellite RNA. Science 231, 1577–1580 (1986). es_ES
dc.description.references Giguère, T., Adkar-Purushothamam, C., Bolduc, F. & Perreault, J. P. Elucidation of the structures of all members of the Avsunviroidae family. Mol. Plant Pathol. 15, 767–779 (2014). es_ES
dc.description.references Sheldon, C. C. & Symons, R. H. Is hammerhead self-cleavage involved in the replication of a virusoid in vivo? Virology 194, 463–474 (1993). es_ES
dc.description.references Biebricher, C. K. & Eigen, M. What is a quasispecies? Curr. Top. Microbiol. Immunol. 299, 1–31 (2006). es_ES
dc.description.references Ojosnegros, S., Perales, C., Mas, A. & Domingo, E. Quasispecies as a matter of fact: viruses and beyond. Virus Res. 162, 203–215 (2011). es_ES
dc.description.references Fekih Hassen, I. et al. Molecular features of new Peach latent mosaic viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA. Virology 360, 50–57 (2007). es_ES
dc.description.references Gazel, M., Ulubas Serce, C., Caglayan, K., Luigi, M. & Faggioli, F. Incidence and genetic diversity of peach latent mosaic viroid isolates in Turkey. J. Plant Pathol. 90, 495–503 (2008). es_ES
dc.description.references Niblett, C. L., Dickson, E., Fernow, K. H., Horst, R. K. & Zaitlin, M. Cross-protection among four viroids. Virology 91, 198–203 (1978). es_ES
dc.description.references Navarro, B. & Flores, R. Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proc. Natl. Acad. Sci. USA 94, 11262–11267 (1997). es_ES
dc.description.references De la Peña, M. & Flores, R. Chrysanthemum chlorotic mottle viroid RNA: dissection of the pathogenicity determinant and comparative fitness of symptomatic and non-symptomatic variants. J. Mol. Biol. 321, 411–421 (2002). es_ES
dc.description.references Carbonell, A., Martínez de Alba, A. E., Flores, R. & Gago, S. Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families. Virology 371, 44–53 (2008). es_ES
dc.description.references Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013). es_ES
dc.description.references Nei, M. & Li, J. Variances of the average numbers of nucleotide substitutions within and between populations. Mol. Biol. Evol. 6, 290–300 (1989). es_ES
dc.description.references Capote, N. et al. Direct sample preparation methods for the detection of Plum pox virus by real-time RT-PCR. Interntl. Microbiol. 12, 1–6 (1999). es_ES


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