Transcriptome analysis identifies strong candidate genes for ginsenoside biosynthesis and reveals its underlying molecular mechanism in Panax ginseng C.A. Meyer

Abstract

Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal herbs for human health and medicine in which ginsenosides are known to play critical roles. The genes from the cytochrome P450 (CYP) gene superfamily have been shown to play important roles in ginsenoside biosynthesis. Here we report genome-wide identification of the candidate PgCYP genes for ginsenoside biosynthesis, development of functional SNP markers for its manipulation and systems analysis of its underlying molecular mechanism. Correlation analysis identified 100 PgCYP genes, including all three published ginsenoside biosynthesis PgCYP genes, whose expressions were significantly correlated with the ginsenoside contents. Mutation association analysis identified that six of these 100 PgCYP genes contained SNPs/InDels that were significantly associated with ginsenosides biosynthesis (P ≤ 1.0e-04). These six PgCYP genes, along with all ten published ginsenoside biosynthesis genes from the PgCYP and other gene families, formed a strong co-expression network, even though they varied greatly in spatio-temporal expressions. Therefore, this study has identified six new ginsenoside biosynthesis candidate genes, provided a genome-wide insight into how they are involved in ginsenoside biosynthesis and developed a set of functional SNP markers useful for enhanced ginsenoside biosynthesis research and breeding in ginseng and related species.

Analysis of the genes controlling three quantitative traits in three diverse plant species reveals the molecular basis of quantitative traits

“…Sequence analysis showed that the genes controlling the same quantitative trait are different in nucleotide sequence and have very different annotations (Supplemental Tables S1-S3). BLASTing the transcriptome of a four-year-old ginseng plant 10,16 using the sequences of the ten ginseng ginsenoside biosynthesis genes as queries revealed that nine (90%) of the 10 genes were alternatively spliced into multiple transcripts and one had a single transcript, with a range of 1-19 transcripts and an average of 6.7 transcripts per gene (Supplemental Table S4). BLASTing the transcriptome of cotton developing fibers 17 using the sequences of the 18 cotton fiber length genes and two Arabidopsis trichrome genes as queries identified that 17 (85%) of the 20 genes were alternatively spliced into multiple transcripts and three each had a single transcript, with a range of 1-69 transcripts and an average of 14.8 transcripts per gene (Supplemental Table S5).…”

Transcriptome-Wide Analysis for Ginsenoside Rb3 Synthesis-Related Genes and Study on the Expression of Methyl Jasmonate Treatment in Panax ginseng

“…To obtain a profile of interested ginsenoside Rb3 synthesis-related genes for its spatiotemporal expression, we conducted preliminary bioinformatics analyses on the transcriptome of Panax ginseng . Based on the existing transcriptome data of Jilin ginseng [ 11 , 40 ], after using the gene expression and trait association analysis methods, candidate genes related to the synthesis of ginsenoside Rb3 were obtained. Their lengths vary from 211 bp to 2603 bp, and their average length is 949 bp.…”

“…We established a network of PgRb3 genes and known key enzyme genes for ginsenoside synthesis. There are 17 known key enzyme genes ( FPS_22 , DS_1 , DS_3 , SE2_4 , SE2_1 , SE2_2 , SS_1 , AS_6 , AS_14 , CAS_13 , CAS_14 , CAS_17 , CAS_23 , CYP716A53v2_1 , CYP716A52v2_3 , CYP716A47_1 , UGT71A27_2 ) [ 40 , 41 ] forming an interaction network, and the network also contains nine PgRb3 genes related to ginsenoside Rb3 synthesis, including PgRb3S01 , PgRb3S03 , PgRb3S07 , PgRb3S10 , PgRb3S11 , PgRb3S12 , PgRb3S16 , PgRb3S17 , and PgRb3S17 . Correlation analysis was performed on the expression levels of all key enzyme genes in the network and nine PgRb3 genes related to ginsenoside Rb3 synthesis ( Figure 7 ).…”

Bioinformatics Exploration of Ginseng: A Review

“…Recently, a dynamic database was built that integrates a draft genome sequence, transcriptome profiles, and annotation datasets of ginseng, which is publicly available (http://ginsengdb.snu.ac.kr/) for the use of scientific community around the globe for exploring the valuable resources for a range of research fields related to P. ginseng and few other species [4]. Transcriptome analysis has identified 100 Panax ginseng cytochrome P450 (PgCYP) genes, whose expressions were significantly correlated with variation of nine mono-and total-ginsenoside contents, while further association study identified five SNPs and three InDels from six PgCYP genes that were significantly associated with the ginsenoside contents in the four-year-old roots of 42 genotypes [9].…”

“…Ginsengs has found therapeutic application such as anti-inflammatory, anti-haemostatic, antioxidant, anticancer, anti-diabetic, antiaging, anti-depressive, immunomodulatory, analgesic, neuroprotection, memory and learning enhancement effects in animals and humans [1,[3][4][5][6][7]. Various computational analyses which include genomics, transcriptomics, proteomics and bioinformatics have been used to study ginseng plant [4,[8][9][10].…”