SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng

Abstract

Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.

Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis

“…Currently, these two sequencing technologies have been used to study different regulatory mechanisms in multiple species. For example, more transcriptional splice events have been found in rice by combining these two technologies [ 15 ], and they have both been used to reveal the complexity of ginsenoside biosynthesis and the transcriptome in Panax notoginseng [ 16 ]. Thus, for the first time, we constructed full-length reference transcriptomes of I. lactea var.…”

A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales

“…The AS type ratios vary in different plants. In Dichocarpum and Arabidopsis , the shares of A3 and A5 were more than that of SE [ 5 ] (Table S1 ), analogous to other dicots such as soybean [ 48 ], Panax notoginseng [ 8 ] and Camellia sinensis var. assamica purple cultivar [ 13 ], among others; the same is true for monocots rice [ 4 ] and moso bamboo [ 49 ].…”

“…One of the deterministic consequences is the adaptive shift of specialized metabolite biosynthesis. For example, 20,015 AS events of 6,324 Panax notoginseng genes were identified in PacBio transcriptome sequencing [ 8 ] (Table S1 ), many of which were associated with the ginsenoside biosynthesis. In the full-length transcriptome of Artemisia annua [ 9 ], 39 isoforms of 15 genes of the artemisinin biosynthesis pathway and upstream MVA and MEP pathways were identified.…”

Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds

“…Subsequently, according to genomic and transcriptomic analyses, sesquiterpenoid synthesis-related genes were found and expressed in specific tissues. Previous studies were conducted to increase Chen et al, 2017;Xu et al, 2017;Zhang D. et al, 2017;Xue et al, 2019;Fan G. et al, 2020;Zhang et al, 2020; the yield of artemisinin by overexpressing the upstream or downstream enzymes, such as FPS and HMGR, but the artemisinin content did not increase significantly. Therefore, this study overexpressed the upstream, midstream and downstream enzymes [HMGR (AA201470), FPS, and DBR2] simultaneously to examine the content of artemisinin, and the revealed that the transgenic plants produced more artemisinin.…”