Subgenomic Identification of miRNAs in Hexaploid Wheat

MicroRNAs (miRNAs) are short non-translated RNAs that are widespread in all branches of eukaryotic life, from single-cell to multicellular organisms. Plant miRNAs, besides acting as regulators of development and morphogenesis, have been recently associated with biotic and abiotic stress responses. Their role in stress response makes them especially interesting for crop improvement.

In this work the prediction of miRNA genes in the hexaploid genome of Triticum aestivumwas carried out for each chromosome arm by using an in-house pre-screening pipeline and the software NOVOMIR, one of the most advanced tools developed in recent years for the identification of putative miRNAs in genomic sequences.

Starting from 10,880,661 contigs, 88,864 contigs have been found to host at least one miRNA candidate precursor (about 0.82% of the total number of contigs). About 270 microRNAs have been identified as putatively coded by the wheat genome. The fraction of miRNAs which are present in all genomes is between 41% and 53%, whereas few miRNAs are present in two genomes. A relevant fraction of miRNAs is present in a single genome, although the exact numbers vary a lot for the various chromosomes: for example, in chromosome 1 the fraction of miRNAs which are present only in genome A is 20%, while this number is as low as 5% in chromosome 2.