MicroRNAs and MlncRNAs Uncovered by Comprehensive Transcriptome Analysis of Panax ginseng

Non-coding RNAs (ncRNAs) are increasingly being characterized as functional regulatory components in plants by deep sequencing. These ncRNAs can be both small (<40 nucleotides, like microRNA) and large (>40 nucleotides, like mlncRNA). However, no information is available for ncRNAs from Panax ginseng, an economically significant medicinal plant species. A small RNA library of pooled roots, stems, leaves and flowers of P. ginseng was subjected to Illumina sequencing. From over 13 million small RNA reads, we identified 72 conserved and 26 non-conserved miRNAs. Further analysis of these miRNA precursors revealed many features, such as two miRNAs are produced from distinct regions of a precursor, two precursors cluster in a transcript, and both sense and antisense transcripts generate miRNAs. Target genes of the conserved and non-conserved miRNAs were predicted and eight of them were experimentally validated using 5’ RACE. Consistently, we identified six dehydration- and eleven heat-responsive miRNAs. Moreover, we identified 3,703 mlncRNAs from the 31,371 assembled EST sequences of P. gingseng. Among them, 22 are conserved with other identified ncRNA. Based on sequence similarity, these mlncRNA can be divided into 246 families, including one having as many as 345 members. About 40 % of the mlncRNAs could potentially be processed into small RNAs. Further analysis showed that some mlncRNAs generated siRNAs from one or both strands, some had long hairpin structure giving rise to siRNAs, and some were potentially tasi-RNAs or miRNA-like precursors. All of these results provide the first clue to the elucidation of non-coding RNA functions in P. ginseng.