De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots

Abstract

Background Panax notoginseng (Burk.) F. H. Chen (PN) belonging to the genus Panax of family Araliaceae is widely used in traditional Chinese medicine to treat various diseases. PN taproot, as the most vital organ for the accumulation of bioactive components, presents a variable morphology (oval or long), even within the same environment. However, no related studies have yet explained the molecular mechanism of phenotypic differences. To investigate the cause of differences in the taproot phenotype, de novo and comparative transcriptomic analysis on PN taproot was performed. Results A total of 133,730,886 and 114,761,595 paired-end clean reads were obtained based on high-throughput sequencing from oval and long taproot samples, respectively. 121,955 unigenes with contig N50 = 1,774 bp were generated by using the de novo assembly transcriptome, 63,133 annotations were obtained with the BLAST. And then, 42 genes belong to class III peroxidase (PRX) gene family, 8 genes belong to L-Ascorbate peroxidase (APX) gene family, and 55 genes belong to a series of mitogen-activated protein kinase (MAPK) gene family were identified based on integrated annotation results. Differentially expressed genes analysis indicated substantial up-regulation of PnAPX3 and PnPRX45, which are related to reactive oxygen species metabolism, and the PnMPK3 gene, which is related to cell proliferation and plant root development, in long taproots compared with that in oval taproots. Furthermore, the determination results of real-time quantitative PCR, enzyme activity, and H2O2 content verified transcriptomic analysis results. Conclusion These results collectively demonstrate that reactive oxygen species (ROS) metabolism and the PnMPK3 gene may play vital roles in regulating the taproot phenotype of PN. This study provides further insights into the genetic mechanisms of phenotypic differences in other species of the genus Panax.

Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis

“…Full-length transcriptome sequencing is widely used for the identification of novel genes, as it provides more information and effectively addresses concerns regarding transcript redundancy and incomplete assembly in NGS technology. For example, Yang et al identified 121,955 unigenes in Panax notoginseng [ 59 ]. Mi et al identified 78,809 unique transcripts in Camellia sinensis , with 65,264 being complete coding sequences [ 60 ].…”

Panax notoginseng Saponins Alleviate Coronary Artery Disease Through Hypermethylation of the miR-194-MAPK Pathway

“…Meanwhile, in vitro experiments demonstrated that the key nodes in the miR-194 promoter-miR-194-MAPK signaling pathway in CAD are changed by PNS. A previous study reported that PNS conferred profound protection through the downregulation of MAPK ( Luo et al, 2021 ; Yang et al, 2022 ). Finally, intervention with PNS is likely to improve apoptosis.…”

Analysis of the transcriptome revealed the molecular mechanisms underlying the growth of Dendrobium nobile under various epiphytic modes

“…To date, GO analysis and KEGG analysis have been extensively employed to elucidate the functional roles of genes in various medicinal plants, including Salvia miltiorrhiza (Chang et al, 2019), Panax notoginseng (Yang et al, 2022), and Polygonum cuspidatum . In this study, GO analysis con rmed that 239 overlapping DEGs were signi cantly enriched in response to chitin, water deprivation, wounding, and other processes.…”