Distribution pattern of small RNA and degradome reads provides information on miRNA gene structure and regulation

Plant microRNAs (miRNAs) have an impact on the regulation of several biological processes such as development, growth and metabolism by negatively controlling gene expression at the post-transcriptional level. However, the role of these small molecules in the symbiotic interaction of plant roots and arbuscular mycorrhizal (AM) fungi remained elusive. To elucidate the role of miRNAs during AM symbiosis we used a deep sequencing approach to analyze the small RNA and degradome sequence tags of Medicago truncatula non-mycorrhizal and mycorrhizal roots. We identified 243 novel Medicago microRNAs and 118 mRNA cleavage targets of miRNA mature and star sequences. Several AM symbiosis-relevant genes were identified as miRNA targets. The transcript of MtNsp2, encoding a GRAS transcription factor involved in the nodule and mycorrhizal signaling pathway, is cleaved by a novel member of the miR171 gene family, namely miR171 h. Here, we carried out a detailed analysis of the genomic structure of the MIR171 h gene comprising our deep sequencing data. The results suggest a feedback circuit between mature miR171 h and its own primary transcript showing the ability of this miRNA to regulate itself.