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De novo transcriptome assembly and characterization of medicinal plant Lithospermum officinale to discover putative genes involved in specialized metabolites biosynthesis

ABSTRACT: In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 3 tissues of L. officinale. RNA sequencing and de novo transcriptome assembly of L. officinale resulted in a total of 77,047 unigenes with N50 value as 1524 bps. KEGG pathway and GO enrichment analysis using highly expressed unigenes across three tissues showed active secondary metabolic processes specifically enriched to the root of L. officinale. Expression of identified candidate unigenes for specialized metabolites biosynthesis were consistent with previous reports on accumulation of metabolites across different tissues of L. officinale.

ORGANISM(S): Lithospermum officinale

PROVIDER: GSE111375 | GEO | 2018/07/01

REPOSITORIES: GEO

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Project description:Background: Dendrobium officinale, an endangered Chinese herb, has extensive therapeutic effects and contains bioactive ingredients including a large number of polysaccharides and alkaloids, and minimal flavonoids. Firstly, this study attempts to obtain the protocorm-like bodies of this plant through tissue culture to produce the main secondary metabolites whose distribution in each organelle and protocorm like bodies is analyzed. Then, analysis of the correlation between comparative transcriptome sequence and the metabolite content in different organs enables the discovery of putative genes encoding enzymes involved in the biosynthesis of polysaccharides and alkaloids, and flavonoids. Results: The optimum condition for protocorm-like bodies (PLBs) induction and propagation of D. officinale is established. For protocorm induction, we use the seed as the explant, and the optimum medium formula for PLBs propagation is 1/2 MS + α-NAA 0.5 mg·L-1 +6-BA 1.0 mg·L-1 + 2, 4-D 1.5-2.0 mg·L-1 + potato juice 100 g·L-1. The distribution of polysaccharides, alkaloids and flavonoids in D. officinale organs was clarified. Stems, PLBs and leaves have the highest content of polysaccharides, alkaloids and flavonoids, respectively. PLBs replace organs to produce alkaloids in D. officinale, and naringenin was only produced in stem. Hot water extraction (HWE) method was found outperforming the ultrasound-assisted extraction (UAE) method for polysaccharides from D. officinale. A comparative transcriptome analysis of the protocorm-like bodies and leaves of D. officinale showed genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids biosynthetic pathway were differentially expressed. Putative genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids synthetic pathway were identified. Notably, genes encoding enzymes of strictosidine beta-glucosidase, geissoschizine synthase and vinorine synthase in alkaloids biosynthesis of D. officinale are first reported. Conclusions: Our works, especially the identification of candidate genes encoding enzymes involved in metabolites biosynthesis will help to explore and protect the endangered genetic resources and will also facilitate further analysis of the molecular mechanism of secondary metabolites’ biosynthesis in D. officinale.

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De novo transcriptome assembly and characterization of medicinal plant Lithospermum officinale to discover putative genes involved in specialized metabolites biosynthesis

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