Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanism underlying taproot thickening in Panax notoginseng

Abstract Background Taproot thickening is a complex biological process and depends on the coordinated expression of the genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb characterized by enlarged taproot as the main organ of saponin accumulation. However, little is known about the molecular mechanism of taproot enlargement. Results A total of 29957 DETs were identified during thickening process of P. notoginseng taproot. GO and KEGG pathway enrichment revealed that DETs associated wthith “plant hormone signal transduction”, “starch and sucrose metabolism”, and “phenylpropanoid biosynthesis” were predominantly enriched. Furher functional analysis by integrating DETs expression profiling, endogenous hormone and primary metabolite identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, Starch branching enzyme I) and primary metabolites (e.g., Sucrose, Glucose, Fructose Malate and Arginine) potentially controlling taproot thickening, and highlighted that hormones crosstalk, transcriptional regulation, homeostasis regulation of sugar and starch, and cell wall metabolism play an important role during thickening process of P. notoginseng taproot. Conclusion These results provide molecular regulatory network of taproot thickening in P. notoginseng and facilitate the characterization of genes responsible for taproot formation in root medicinal plants or crops.