Dissecting microRNAs in Wheat Chromosome 5D Using Next Generation Sequencing Data

microRNAs (miRNAs) are endogenous, small non-coding RNAs that act as post-transcriptional regulators thus have essential roles in diverse biological functions. A subgenomic miRNA analysis was performed on 454 GS FLX Titanium sequences generated from wheat flow-sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms respectively. Bioinformatic analysis revealed a total of 55 miRNAs, 14 of which were reported in wheat for the first time. The long and short arms of the chromosome were shown to harbor coding regions for 48 and 42 miRNAs respectively, and to possess 35 of them in common. Similarly, representation was observed to be higher in 5DL (1,949) compared to 5DS (1,191). Each miRNA was found to have a putative target and EST analysis gave evidence of expression for 6 miRNAs. Additionally, miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS suggesting that miRNAs are less conserved in syntenic regions. In addition to computational analysis, five miRNA coding regions (miR6220, miR5070, miR169, miR5085 and miR2118) were experimentally verified to be located on 5D having three of them (miR2118, miR169 and miR5085) specific to this chromosome. Also miR2118 was found to be expressed in adult wheat leaves. Mining of miRNAs holds great importance in providing a better understanding of wheat gene regulation.