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

Abstract

BackgroundTaproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood.ResultsA total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with “plant hormone signal transduction,” “starch and sucrose metabolism,” and “phenylpropanoid biosynthesis” were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng.ConclusionThe results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.

Hormonal and transcriptional analyses provides new insights into the molecular mechanisms underlying root thickening and isoflavonoid biosynthesis in Callerya speciosa (Champ. ex Benth.) Schot

“…5 ; Supplementary Table S3 ), suggesting that sucrose catabolism is necessary for root rapid-thickening in C. speciosa. Similar results were obtained in Panax notoginseng 20 , Cyperus esculentus 30 , and radish 31 . Glucan endo-1,3-beta-glucosidase (elgC) is widely distributed in higher plants, which is responsible for hydrolysis of the glycosidic bond in specific polysaccharides with tracts of unsubstituted β-1,3-linked glucosyl residues to release glucose 32 .…”

“…Large numbers of DEGs were involved in similar molecular processes during the development of tuberous roots (Fig. 3 ), a dynamic process controlled by plant hormones, TFs and metabolism regulation pathways 20 .…”

“…Most transcripts encoding Aux/IAA genes responsible for cambium secondary differentiation during radish taproot thickening were down-regulated, while those encoding ARFs genes and two SAUR transcripts were up-regulated at the cortex splitting and expanding stage 24 . Researchers suggested that the endogenous IAA content and genes involved in auxins signaling pathway, including Aux/IAAs and ARFs were highly expressed in expansion stage 20 , 25 . Congruent with previous studies, 6 Aux/IAAs , 4 SAURs, 2 ARFs and 2 CH3s , were highly expressed at the rapid thickening stage (12 and 18 MAG) in this study (Fig.…”

“…Gene encoding GID1-like gibberellin receptor ( StGID1 ) was significantly up-regulated in the sample pair potato grafted with tomato (St-R) vs self-grafted potato (St-WT) during stolon development, which was consistent with GA 3 content 12 . In addition, ABA and GAs were reported to antagonistically mediate tuberization in several species of plants, such as potato 11 , sweet potato 22 and P. notoginseng 20 . The GA 3 levels increased at the rapid-thickening stages of tuberous roots (12 and 18 MAG), whereas the ABA content showed gradual increase along with the process of tuberous root development in this study (Fig.…”

Stigmasterol Biosynthesis Pathway is Associated With the Dehiscence Process in Panax Ginseng Seeds

“…In addition, the retention indices and mass spectra are highly repeatable, and the available mass spectra libraries could facilitate the putative identi cation of GC-MS spectra peaks with high con dence [20]. Most metabolomic and transcriptomic studies on ginseng have focused on the roots [21][22][23], with hardly any such investigations conducted on the seeds, which are essential for the propagation of the highly valued medicinal plant.…”