De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis

Abstract

Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. We identified differentially expressed genes (DEGs) based on expression profile analysis. These DEGs exhibited higher expression levels in flower tissue than in leaf, stem or root tissues. We identified and analyzed numerous genes encoding enzymes involved in coumarin biosynthesis, and verified genes encoding key enzymes using quantitative real-time PCR. Our transcriptome data will make great contributions to research on C. monnieri and provide clues for identifying candidate genes involved in coumarin metabolic pathways.

The chromosome‐level genome of female ginseng (Angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis

“…The integrated simple coumarin biosynthesis pathway was proposed in Cnidium monnieri (Shi et al., 2020) and Angelica dahurica (Zhao et al., 2021). In our study, we discovered 46 genes in simple coumarin biosynthesis in A. sinensis (Figure 4c) and thus supplied a more intact biosynthesis pathway.…”

Anabolic metabolism of autotoxic substance coumarins in plants

“…Moreover, MYB72 may regulate the synthesis of scopoletin in roots ( Stringlis, De Jonge & Pieterse, 2019 ). Shi et al. (2020) also analyzed transcriptomic data from different tissues of Cnidium monnieri and identified a large number of genes encoding enzymes related to coumarin biosynthesis.…”

Two O-Methyltransferases Mediate Multiple Methylation Steps in the Biosynthesis of Coumarins in Cnidium monnieri

“…According to previous reports, 1 is accumulated much more in the flowers than in the leaves, stems, and roots of C. monnieri. 20 Thus, the expression of the methyltransferase genes that are related to 1 may be up-regulated in the flowers. We analyzed the sequences annotated as OMT in public C. monnieri transcriptome data.…”

“…We analyzed the sequences annotated as OMT in public C. monnieri transcriptome data. 20 Sixty-eight gene sequences were up-regulated in flowers comparing to tissues of leaves, stems, or roots (Figure S2.2A). We narrowed 68 OMT genes to 33 genes by further filtering the amino acid sequences of the open reading frames (ORFs) (>200 amino acids in size).…”

“…Thus, the expression of the methyltransferase genes that are related to 1 may be up-regulated in the flowers. We analyzed the sequences annotated as OMT in public C. monnieri transcriptome data . Sixty-eight gene sequences were up-regulated in flowers comparing to tissues of leaves, stems, or roots (Figure S2.2A).…”