Comparative Analysis and Functional Identification of Rhizome miRNAs of Two Atractylodes lancea Ecotypes

Plant microRNAs (miRNAs) are short, non-coding RNA molecules. They mediate RNA silencing and regulate a series of target mRNAs involved in plant development, metabolism, and responses to different ecological environments. As one of important medicinal plants, Atractylodes lancea has a high medicinal significance and commercial value. Mao and Dabie are two ecotypes of A. lancea which mainly distributes in Mao Mountain and Dabie Mountain, respectively. To better understand the genomic information and germplasm resource characteristics, miRNA profiling analysis by high-throughput sequencing was performed to identify rhizome miRNAs of two A. lancea ecotypes. A transcriptomic database was established to identify miRNAs precursors and their target transcripts. By comparing small RNAs and the transcriptomic database, 270 known miRNAs of 46 miRNA families and 91 novel miRNAs were identified, plus hundreds of putative targets. Using Mireap software, 5 and 12 of 22 significant differentially expressed miRNAs were involved in ecotype formation and terpenoid metabolism, respectively, which was verified by qRT-PCR tests. These results are an important resource to better understand the biological mechanism of terpene formation and A. lancea adaptation to different ecological environment .