title: Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing.
abstract: 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.
authors.affiliation: Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Pablo
authors.initials: P
authors.lastname: Peláez
authors.forename: Minerva S
authors.initials: MS
authors.lastname: Trejo
authors.forename: Luis P
authors.initials: LP
authors.lastname: Iñiguez
authors.forename: Georgina
authors.initials: G
authors.lastname: Estrada-Navarrete
authors.forename: Alejandra A
authors.initials: AA
authors.lastname: Covarrubias
authors.forename: José L
authors.initials: JL
authors.lastname: Reyes
authors.forename: Federico
authors.initials: F
authors.lastname: Sanchez
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics*; D009928:Organ Specificity; D027805:Phaseolus / Q000235:genetics*; D059368:RNA Isoforms / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D059368:RNA Isoforms; D012322:RNA Precursors; D018749:RNA, Plant