title: Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis.
abstract: BACKGROUND
  microRNAs or miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance, and there have been no previous studies concerning its gene expression and regulation. To date, no miRNAs have been reported in Myrtaceae species.
  
  
  RESULTS
  Small RNA and RNA-seq libraries were constructed to identify miRNAs and pre-miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library, and the data obtained were analyzed using bioinformatics tools. From 14,489,131 small RNA clean reads, we obtained 1,852,722 mature miRNA sequences representing 45 conserved families that have been identified in other plant species. Further analysis using contigs assembled from RNA-seq allowed the prediction of secondary structures of 25 known and 17 novel pre-miRNAs. The expression of twenty-seven identified miRNAs was also validated using RT-PCR assays. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology.
  
  
  CONCLUSIONS
  This study is the first large scale identification of miRNAs and their potential targets from a species of the Myrtaceae family without genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights species-specific miRNAs.
authors.affiliation: PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Frank
authors.initials: F
authors.lastname: Guzman
authors.forename: Mauricio P
authors.initials: MP
authors.lastname: Almerão
authors.forename: Ana P
authors.initials: AP
authors.lastname: Körbes
authors.forename: Guilherme
authors.initials: G
authors.lastname: Loss-Morais
authors.forename: Rogerio
authors.initials: R
authors.lastname: Margis
mesh_terms: D019295:Computational Biology; D017124:Conserved Sequence; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D027842:Syzygium / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant