Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

Initial Computational Prediction Of MicroRNAs In Flax (Linum usitatissimum)

Tiffanie Moss , Christopher A Cullis

  Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106

Small RNAs have been shown to directly regulate mRNAs, chromatin remodeling, transcription factors and micronuclear rearrangement in ciliates, and understanding of the regulatory capabilities of small RNAs continues to grow. In some flax varieties, the genome has the ability to rapidly respond to nutrient stress in a stable and heritable way with one example being the insertion, Linum insertion sequence-1 (LIS-1). Ab initio data on LIS-1 suggests small RNA activity may be associated with the ability to adapt in this way. To address the possibility that small RNAs are involved in this adaptive mechanism, miRNAs have been computationally identified from the flax genome sequence.
Many miRNAs are hypothesized to be in low abundance and therefore unavailable in the Plant MiRNA Database (PRMD). The FindmiRNA algorithm was used in the ab initio approach to identify putative miRNAs based on structural conformations consistent with miRNA precursors. The Vmatch algorithm was used in the evidenced-based approach to identify miRNAs on the basis of sequence homology to known mature miRNAs and miRNA hairpins in the PRMD. This work will correlate the number of miRNAs consistent with those in the PMRD and the putative miRNAs identified using FindMiRNA which do not match the database, that may have novel functions but still need to be validated. Finally, the distribution of miRNA genes throughout the genome as well as the distribution of the expected target genes of these miRNAs will be examined.