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Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing
BACKGROUND: MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have been identified in the model food legume Phaseolus vulgaris (common bean). Recent...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359237/ https://www.ncbi.nlm.nih.gov/pubmed/22394504 http://dx.doi.org/10.1186/1471-2164-13-83 |
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author | Peláez, Pablo Trejo, Minerva S Iñiguez, Luis P Estrada-Navarrete, Georgina Covarrubias, Alejandra A Reyes, José L Sanchez, Federico |
author_facet | Peláez, Pablo Trejo, Minerva S Iñiguez, Luis P Estrada-Navarrete, Georgina Covarrubias, Alejandra A Reyes, José L Sanchez, Federico |
author_sort | Peláez, Pablo |
collection | PubMed |
description | BACKGROUND: MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have been identified in the model food legume Phaseolus vulgaris (common bean). Recent advances in next generation sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used Illumina's sequencing by synthesis (SBS) technology to identify and characterize the miRNA population of Phaseolus vulgaris. RESULTS: Small RNA libraries were generated from roots, flowers, leaves, and seedlings of P. vulgaris. Based on similarity to previously reported plant miRNAs,114 miRNAs belonging to 33 conserved miRNA families were identified. Stem-loop precursors and target gene sequences for several conserved common bean miRNAs were determined from publicly available databases. Less conserved miRNA families and species-specific common bean miRNA isoforms were also characterized. Moreover, novel miRNAs based on the small RNAs were found and their potential precursors were predicted. In addition, new target candidates for novel and conserved miRNAs were proposed. Finally, we studied organ-specific miRNA family expression levels through miRNA read frequencies. CONCLUSIONS: This work represents the first massive-scale RNA sequencing study performed in Phaseolus vulgaris to identify and characterize its miRNA population. It significantly increases the number of miRNAs, precursors, and targets identified in this agronomically important species. The miRNA expression analysis provides a foundation for understanding common bean miRNA organ-specific expression patterns. The present study offers an expanded picture of P. vulgaris miRNAs in relation to those of other legumes. |
format | Online Article Text |
id | pubmed-3359237 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-33592372012-05-24 Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing Peláez, Pablo Trejo, Minerva S Iñiguez, Luis P Estrada-Navarrete, Georgina Covarrubias, Alejandra A Reyes, José L Sanchez, Federico BMC Genomics Research Article BACKGROUND: MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have been identified in the model food legume Phaseolus vulgaris (common bean). Recent advances in next generation sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used Illumina's sequencing by synthesis (SBS) technology to identify and characterize the miRNA population of Phaseolus vulgaris. RESULTS: Small RNA libraries were generated from roots, flowers, leaves, and seedlings of P. vulgaris. Based on similarity to previously reported plant miRNAs,114 miRNAs belonging to 33 conserved miRNA families were identified. Stem-loop precursors and target gene sequences for several conserved common bean miRNAs were determined from publicly available databases. Less conserved miRNA families and species-specific common bean miRNA isoforms were also characterized. Moreover, novel miRNAs based on the small RNAs were found and their potential precursors were predicted. In addition, new target candidates for novel and conserved miRNAs were proposed. Finally, we studied organ-specific miRNA family expression levels through miRNA read frequencies. CONCLUSIONS: This work represents the first massive-scale RNA sequencing study performed in Phaseolus vulgaris to identify and characterize its miRNA population. It significantly increases the number of miRNAs, precursors, and targets identified in this agronomically important species. The miRNA expression analysis provides a foundation for understanding common bean miRNA organ-specific expression patterns. The present study offers an expanded picture of P. vulgaris miRNAs in relation to those of other legumes. BioMed Central 2012-03-06 /pmc/articles/PMC3359237/ /pubmed/22394504 http://dx.doi.org/10.1186/1471-2164-13-83 Text en Copyright ©2012 Peláez et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Peláez, Pablo Trejo, Minerva S Iñiguez, Luis P Estrada-Navarrete, Georgina Covarrubias, Alejandra A Reyes, José L Sanchez, Federico Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing |
title | Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing |
title_full | Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing |
title_fullStr | Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing |
title_full_unstemmed | Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing |
title_short | Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing |
title_sort | identification and characterization of micrornas in phaseolus vulgaris by high-throughput sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359237/ https://www.ncbi.nlm.nih.gov/pubmed/22394504 http://dx.doi.org/10.1186/1471-2164-13-83 |
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