Identification of potential miRNAs and their targets in Vriesea carinata (Poales, Bromeliaceae)

Plant Sci. 2013 Sep:210:214-23. doi: 10.1016/j.plantsci.2013.05.013. Epub 2013 Jun 2.

Abstract

The miRNAs play important roles in regulation of gene expression at the post-transcriptional level. A small RNA and RNA-seq of libraries were constructed to identify miRNAs in Vriesea carinata, a native bromeliad species from Brazilian Atlantic Rainforest. Illumina technology was used to perform high throughput sequencing and data was analyzed using bioinformatics tools. We obtained 2,191,509 mature miRNAs sequences representing 54 conserved families in plant species. Further analysis allowed the prediction of secondary structures for 19 conserved and 16 novel miRNAs. Potential targets were predicted from pre-miRNAs by sequence homology and validated using RTqPCR approach. This study provides the first identification of miRNAs and their potential targets of a bromeliad species.

Keywords: High-throughput sequencing; MFEI; Stress response; Vriesea carinata; miRNA; miRNAs; microRNA; microRNA precursor; minimal folding energy index; nt; nucleotides; pre-miRNA; sRNA; small RNA; vca.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Brazil
  • Bromeliaceae / genetics*
  • Bromeliaceae / metabolism
  • Conserved Sequence
  • Gene Expression Regulation, Plant
  • Gene Library
  • Genes, Plant / genetics
  • High-Throughput Nucleotide Sequencing
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Nucleic Acid Conformation
  • RNA, Plant / chemistry
  • RNA, Plant / genetics
  • RNA, Plant / metabolism
  • Sequence Alignment
  • Sequence Analysis, RNA
  • Stress, Physiological

Substances

  • MicroRNAs
  • RNA, Plant

Associated data

  • GEO/GSE38250