INESC-ID   Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa
technology from seed


Knowledge Discovery and Bioinformatics
Inesc-ID Lisboa

Identification of microRNAs and analysis of their expression in Eucalyptus globulus

04/12/2013 - 11:00
04/12/2013 - 12:00

Portugal is one the largest producers of pulp derived from Eucalyptus
globulus, making it a fun- damental species for the country. The
selection of adequate genotypes would make the exploitation of
cultivation areas more efficient. A key objective is to understand the
regulatory mechanisms impacting wood characteristics. Here we focus on
microRNA-mediated regulation. MicroRNAs are endogenous molecules that
act by silencing targeted messenger RNAs. Although approximately
21,000 microRNAs have been identified for many species, none is
documented for the Eucalyptus genus. Here, we propose a pipeline that
makes use of Cravela, a single-genome miRNA finding tool, and a new
NGS data analysis algorithm that provides a novel scoring function to
evaluate the expression profile of candidates. This approach produced
a short list of candidates, including both conserved and non-conserved
sequences. Experimental validation showed amplification in 4 out of 5
candidates chosen from the best-scoring non-conserved sequences.