Molecular basis of Pogostemon cablin responding to continuous cropping obstacles revealed by integrated transcriptomic, miRNA and metabolomic analyses

Pogostemon cablin (patchouli) suffers from continuous cropping obstacles in cultivation. To obtain new insights into molecular mechanisms, we performed the integrated analyses of transcriptome, miRNA and metabolite data of patchouli leaves in parallel at different levels of continuous cropping. Our results showed that continuous cropping has caused significant gene expression and metabolite changes in patchouli. A total of 49,825 genes, 57 miRNAs and 325 metabolites with significantly differential abundance were identified by pairwise comparisons samples from different planting patterns at the same growth stage. We found that continuous cropping has significantly reduced the expression levels of the late elongated hypocotyl (LHY), phytochrome (PHY), cryptochrome (CRY), and PSI and PSII complex genes, inhibiting photosynthesis and the normal growth of patchouli. miRNA-Seq analyses showed that miR172, miR319, miR397 and two novel miRNAs (novel5 and novel18) might involve in the development of continuous cropping obstacles. In addition, liquid chromatography-mass spectrometry (LC-MS) data showed that continuous cropping has significantly changed the accumulation of metabolites, such as prenol lipids, organooxygen compounds, flavonoids, carboxylic acids and derivatives, and cinnamic acids and derivatives in patchouli. The integrated transcriptomic and metabolomic analyses revealed a significant correlation between differentially expressed genes (DEGs) and differential metabolites (DEM) in the phenylpropanoid biosynthesis pathway under continuous cropping stress. The obtained results will help to elucidate potential molecular mechanisms of continuous cropping obstacles towards developing new control methods to improve the yield and quality of continuous cropping plants.