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High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs

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High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs

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dc.contributor.author Martínez Navarro, Germán es_ES
dc.contributor.author Forment Millet, José Javier es_ES
dc.contributor.author Llave, Cesar es_ES
dc.contributor.author Pallás Benet, Vicente es_ES
dc.contributor.author Gomez, Gustavo Germán es_ES
dc.date.accessioned 2013-05-06T13:38:27Z
dc.date.available 2013-05-06T13:38:27Z
dc.date.issued 2011
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10251/28589
dc.description.abstract [EN] Micro RNAS (miRNAs) are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance. Here we report a combined approach of bioinformatics prediction, high-throughput sequencing data and molecular methods to analyze miRNAs populations in cucumber (Cucumis sativus) plants. A set of 19 conserved and 6 known but non-conserved miRNA families were found in our cucumber small RNA dataset. We also identified 7 (3 with their miRNA* strand) not previously described miRNAs, candidates to be cucumber-specific. To validate their description these new C. sativus miRNAs were detected by northern blot hybridization. Additionally, potential targets for most conserved and new miRNAs were identified in cucumber genome. In summary, in this study we have identified, by first time, conserved, known non-conserved and new miRNAs arising from an agronomically important species such as C. sativus. The detection of this complex population of regulatory small RNAs suggests that similarly to that observe in other plant species, cucumber miRNAs may possibly play an important role in diverse biological and metabolic processes. es_ES
dc.description.sponsorship This work was supported by grant BIO2008-03528 from the Spanish granting agency DGICYT and by grant ACOMP/2010/214 from the Generalitat Valenciana. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. en_EN
dc.language Inglés es_ES
dc.publisher Public Library of Science es_ES
dc.relation.ispartof PLoS ONE es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Arabidopsis-Thaliana es_ES
dc.subject Plant micrornas es_ES
dc.subject Messenger-rna es_ES
dc.subject Genes es_ES
dc.subject Identification es_ES
dc.subject Evolution es_ES
dc.subject Targets es_ES
dc.subject Annotation es_ES
dc.subject Expression es_ES
dc.subject Cleavage es_ES
dc.subject.classification BIOQUIMICA Y BIOLOGIA MOLECULAR es_ES
dc.title High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1371/journal.pone.0019523
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//BIO2008-03528/ES/INTERACCIONES PATOGENO-HUESPED EN EL TRANSPORTE CELULAR Y VASCULAR DE VIRUS DE INTERES AGRONOMICO./ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GVA//ACOMP%2F2010%2F214/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia 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 Martínez Navarro, G.; Forment Millet, JJ.; Llave, C.; Pallás Benet, V.; Gomez, GG. (2011). High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS ONE. 5(6):19523-19523. https://doi.org/10.1371/journal.pone.0019523 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1371/journal.pone.0019523 es_ES
dc.description.upvformatpinicio 19523 es_ES
dc.description.upvformatpfin 19523 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 5 es_ES
dc.description.issue 6 es_ES
dc.relation.senia 217469
dc.identifier.pmid 21603611 en_EN
dc.identifier.pmcid PMC3095615 en_EN
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.contributor.funder Generalitat Valenciana es_ES
dc.description.references Llave, C. (2002). Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA. Science, 297(5589), 2053-2056. doi:10.1126/science.1076311 es_ES
dc.description.references Reinhart, B. J. (2002). MicroRNAs in plants. Genes & Development, 16(13), 1616-1626. doi:10.1101/gad.1004402 es_ES
dc.description.references Xie, Z., Khanna, K., & Ruan, S. (2010). Expression of microRNAs and its regulation in plants. Seminars in Cell & Developmental Biology, 21(8), 790-797. doi:10.1016/j.semcdb.2010.03.012 es_ES
dc.description.references Jones-Rhoades, M. W., Bartel, D. P., & Bartel, B. (2006). MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS. Annual Review of Plant Biology, 57(1), 19-53. doi:10.1146/annurev.arplant.57.032905.105218 es_ES
dc.description.references Allen, E., Xie, Z., Gustafson, A. M., Sung, G.-H., Spatafora, J. W., & Carrington, J. C. (2004). Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics, 36(12), 1282-1290. doi:10.1038/ng1478 es_ES
dc.description.references Fahlgren, N., Howell, M. D., Kasschau, K. D., Chapman, E. J., Sullivan, C. M., Cumbie, J. S., … Carrington, J. C. (2007). High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes. PLoS ONE, 2(2), e219. doi:10.1371/journal.pone.0000219 es_ES
dc.description.references Rajagopalan, R., Vaucheret, H., Trejo, J., & Bartel, D. P. (2006). A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes & Development, 20(24), 3407-3425. doi:10.1101/gad.1476406 es_ES
dc.description.references Moxon, S., Jing, R., Szittya, G., Schwach, F., Rusholme Pilcher, R. L., Moulton, V., & Dalmay, T. (2008). Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research, 18(10), 1602-1609. doi:10.1101/gr.080127.108 es_ES
dc.description.references Szittya, G., Moxon, S., Santos, D. M., Jing, R., Fevereiro, M. P., Moulton, V., & Dalmay, T. (2008). High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics, 9(1), 593. doi:10.1186/1471-2164-9-593 es_ES
dc.description.references Song, C., Wang, C., Zhang, C., Korir, N., Yu, H., Ma, Z., & Fang, J. (2010). Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics, 11(1), 431. doi:10.1186/1471-2164-11-431 es_ES
dc.description.references AMBROS, V. (2003). A uniform system for microRNA annotation. RNA, 9(3), 277-279. doi:10.1261/rna.2183803 es_ES
dc.description.references Meyers, B. C., Axtell, M. J., Bartel, B., Bartel, D. P., Baulcombe, D., Bowman, J. L., … Zhu, J.-K. (2008). Criteria for Annotation of Plant MicroRNAs. The Plant Cell, 20(12), 3186-3190. doi:10.1105/tpc.108.064311 es_ES
dc.description.references Tanurdzic, M. (2004). Sex-Determining Mechanisms in Land Plants. THE PLANT CELL ONLINE, 16(suppl_1), S61-S71. doi:10.1105/tpc.016667 es_ES
dc.description.references Lough, T. J., & Lucas, W. J. (2006). INTEGRATIVE PLANT BIOLOGY: Role of Phloem Long-Distance Macromolecular Trafficking. Annual Review of Plant Biology, 57(1), 203-232. doi:10.1146/annurev.arplant.56.032604.144145 es_ES
dc.description.references Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., … Ni, P. (2009). The genome of the cucumber, Cucumis sativus L. Nature Genetics, 41(12), 1275-1281. doi:10.1038/ng.475 es_ES
dc.description.references MARTINEZ, G., DONAIRE, L., LLAVE, C., PALLAS, V., & GOMEZ, G. (2010). High-throughput sequencing ofHop stunt viroid-derived small RNAs from cucumber leaves and phloem. Molecular Plant Pathology, 11(3), 347-359. doi:10.1111/j.1364-3703.2009.00608.x es_ES
dc.description.references Moxon, S., Schwach, F., Dalmay, T., MacLean, D., Studholme, D. J., & Moulton, V. (2008). A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24(19), 2252-2253. doi:10.1093/bioinformatics/btn428 es_ES
dc.description.references Morin, R. D., Aksay, G., Dolgosheina, E., Ebhardt, H. A., Magrini, V., Mardis, E. R., … Unrau, P. J. (2008). Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Research, 18(4), 571-584. doi:10.1101/gr.6897308 es_ES
dc.description.references Sunkar, R., Zhou, X., Zheng, Y., Zhang, W., & Zhu, J.-K. (2008). Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biology, 8(1), 25. doi:10.1186/1471-2229-8-25 es_ES
dc.description.references Frazier, T. P., Xie, F., Freistaedter, A., Burklew, C. E., & Zhang, B. (2010). Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta, 232(6), 1289-1308. doi:10.1007/s00425-010-1255-1 es_ES
dc.description.references Wang, Y., Li, P., Cao, X., Wang, X., Zhang, A., & Li, X. (2009). Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochemical and Biophysical Research Communications, 378(4), 799-803. doi:10.1016/j.bbrc.2008.11.140 es_ES
dc.description.references Poethig, R. S. (2009). Small RNAs and developmental timing in plants. Current Opinion in Genetics & Development, 19(4), 374-378. doi:10.1016/j.gde.2009.06.001 es_ES
dc.description.references Voinnet, O. (2009). Origin, Biogenesis, and Activity of Plant MicroRNAs. Cell, 136(4), 669-687. doi:10.1016/j.cell.2009.01.046 es_ES
dc.description.references Husbands, A. Y., Chitwood, D. H., Plavskin, Y., & Timmermans, M. C. P. (2009). Signals and prepatterns: new insights into organ polarity in plants. Genes & Development, 23(17), 1986-1997. doi:10.1101/gad.1819909 es_ES
dc.description.references SHABALINA, S., & KOONIN, E. (2008). Origins and evolution of eukaryotic RNA interference. Trends in Ecology & Evolution, 23(10), 578-587. doi:10.1016/j.tree.2008.06.005 es_ES
dc.description.references Axtell, M. J., & Bowman, J. L. (2008). Evolution of plant microRNAs and their targets. Trends in Plant Science, 13(7), 343-349. doi:10.1016/j.tplants.2008.03.009 es_ES
dc.description.references Vazquez, F., Blevins, T., Ailhas, J., Boller, T., & Meins, F. (2008). Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Research, 36(20), 6429-6438. doi:10.1093/nar/gkn670 es_ES
dc.description.references Yao, Y., Guo, G., Ni, Z., Sunkar, R., Du, J., Zhu, J.-K., & Sun, Q. (2007). Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biology, 8(6), R96. doi:10.1186/gb-2007-8-6-r96 es_ES
dc.description.references Klevebring, D., Street, N. R., Fahlgren, N., Kasschau, K. D., Carrington, J. C., Lundeberg, J., & Jansson, S. (2009). Genome-wide profiling of Populus small RNAs. BMC Genomics, 10(1), 620. doi:10.1186/1471-2164-10-620 es_ES
dc.description.references Rymarquis, L. A., Kastenmayer, J. P., Hüttenhofer, A. G., & Green, P. J. (2008). Diamonds in the rough: mRNA-like non-coding RNAs. Trends in Plant Science, 13(7), 329-334. doi:10.1016/j.tplants.2008.02.009 es_ES
dc.description.references Alves-Junior, L., Niemeier, S., Hauenschild, A., Rehmsmeier, M., & Merkle, T. (2009). Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Research, 37(12), 4010-4021. doi:10.1093/nar/gkp272 es_ES
dc.description.references Beauclair, L., Yu, A., & Bouché, N. (2010). microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. The Plant Journal, 62(3), 454-462. doi:10.1111/j.1365-313x.2010.04162.x es_ES
dc.description.references Gómez, G., & Pallás, V. (2007). Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants. The Plant Journal, 51(6), 1041-1049. doi:10.1111/j.1365-313x.2007.03203.x es_ES


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