An organ-specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways

Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome-wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ-specifically expressed, and 13 of these miRNAs could perform organ-specific target regulation. More than 80% of the phasiRNA loci were organ-specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ-specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber-specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme-coding genes of the β-elemene biosynthetic pathway showed that the downstream genes were tuber-specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β-elemene biosynthesis. Summarily, our report provided an organ-specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.