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.
Highlights
Panax notoginseng is one of the most widely used traditional Chinese herbs with valued roots
Our results demonstrate that this whole-genome duplication (WGD) event occurred in the common ancestor of the studied Panax species, which is strongly supported by the tetraploid P. ginseng genome analysis that revealed such a shared WGD event in the Panax lineage at 28 Million Years Ago (MYA) (Pg-β)[69]
We identified more alternative splicing (AS) events from long single molecular real time (SMRT) reads than short Illumina reads, including a large number of AS events associated with the MEP- and mevalonic acid (MVA-)dependent pathways of the ginsenoside biosynthesis
Summary
Panax notoginseng is one of the most widely used traditional Chinese herbs with valued roots. The P. notoginseng transcriptomes were generated by taking advantage of SGS-based RNA-Seq for roots, leaves, and flowers, of which a number of genes involved in the ginsenoside biosynthesis were preliminarily identified[18,19]. PacBio sequencing platform offers much longer read lengths, which eliminate the need for computational assemblies of transcriptomes This sequencing technology has been extensively applied to an increasing number of plant species, such as rice23, soybean[24], Salvia miltiorrhiza[25], Sorghum bicolor[26], Zea mays[27], Coffea arabica[28], Fragaria vesca[29], and Phyllostachys edulis[30], Populus31, switchgrass[32] and Ricinus communis[33] to better characterize the complexity of transcriptomes but not yet in P. notoginseng
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