Identification Of Differentially Expressed Mirnas In Response To White Light Signal In Lithospermum Erythrorhizon Cells

Light signal plays a key negative regulatory role in the biosynthesis of shikonin and its derivatives which are important pharmaceutical secondary metabolites in Lithospermum erythrorhizon. Although microRNAs (miRNAs) could regulate multiple biological and metabolic processes, the miRNAs involved in the light-regulated shikonin formation still remain unclear. In the present study, we constructed two small RNA libraries of L. erythrorhizon callus cells cultured under different light conditions (Dark, White light) and carried out high-throughput sequencing using Miseq platform. From a total of 11,909,475 raw reads, we acquired a global miRNA profiling of L. erythrorhizon in response to different light conditions. A total of 32 annotated miRNA families and 50 putative miRNA-targeted transcripts were identified. A total of 18 miRNAs were differentially expressed in the Dark vs White light small RNA libraries, and their putative target genes were involved in FERONIA signaling, phytohormone signaling, etc. The expression levels of some important miRNAs under different light conditions and the target TCP transcription factor of miR319 were validated by Q-PCR and RLM-RACE, respectively. We further proposed a possible regulatory pathways of light-responsive miRNA implicated in shikonin biosynthesis. Our results provide new insights into the regulation of shikonin biosynthesis in L. erythrorhizon.