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MicroRNAs (miRNAs) are among the class of noncoding small RNA molecules and play a crucial role in post-transcriptional regulation in plants. Although  Lilium  is one of the most popular ornamental flowers worldwide, however, there is no report on miRNAs identification. In the present study, therefore, miRNAs and their targets were identified from flower, leaf, bulblet and bulb of  Lilium lancifolium  Thunb. by high-throughput sequencing and bioinformatics analysis. In this study, a total of 38 conserved miRNAs belonging to 17 miRNA families and 44 novel miRNAs were identified. In total, 366 target genes for conserved miRNAs and 415 target genes for novel miRNAs were predicted. The majority of the target genes for conserved miRNAs were transcriptional factors and novel miRNAs targeted mainly protein coding genes. A total of 53 cleavage sites belonging to 6 conserved miRNAs families and 14 novel miRNAs were identified using degradome sequencing. Twenty-three miRNAs were randomly selected, then, their credibility was confirmed using northern blot or stem-loop qRT-PCR. The results from qRT-PCR analysis showed the expression pattern of 4 LL-miRNAs was opposite to their targets. Therefore, our finding provides an important basis to understand the biological functions of miRNAs in  Lilium .

Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing