Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal

We adopted a deep sequencing approach developed by Solexa (Illumina Inc., San Diego, CA, USA) to investigate global expression and complexity of microRNAs (miRNAs) and their targets from Medicago truncatula. Two small RNA libraries and two degradome libraries were constructed from mercury (Hg)-treated and Hg-free M. truncatula seedlings. For miRNAs, each library generated 18.518.6 million short sequences, resulting in 10.210.8 million clean reads. At least 52 new miRNA candidates with similar to 21 nucleotides are perfectly matched to the M. truncatula genome. Statistical analysis on transcript abundance of the new candidate miRNAs revealed that most of them were differentially regulated by the heavy metal mercury Hg(II), with 12 miRNAs being specifically induced by Hg exposure. Additionally, we identified 201 individual miRNAs representing 63 known M. truncatula miRNA families, including 12 new conserved and one non-conserved miRNAs that have not been described before. Finally, 130 targets for 58 known (37 conserved and 21 non-conserved) miRNA families and 37 targets for 18 new M. truncatula-specific candidate miRNA families were identified by high-throughput degradome sequencing approach.