Investigation of Enzymes in the Phthalide Biosynthetic Pathway in Angelica sinensis Using Integrative Metabolite Profiles and Transcriptome Analysis

Feng, Wei-Meng; Liu, Pei; Yan, Hui; Yu, Guang; Zhang, Sen; Jiang, Shu; Shang, Erxin; Qian, Dawei; Duan, Jin‐Ao

doi:10.3389/fpls.2022.928760

Cited by 9 publications

(6 citation statements)

References 40 publications

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“…Previous studies have identified a key factor, phospho-2-dehydro-3-deoxyheptonate aldolase, that may be involved in accumulation of phthalides in A. sinensis [ 13 ]. Through expression profiling analysis, we found that the expression level of this gene was greater in unbolted samples than in bolted samples (Fig.…”

Section: Platform Contentsmentioning

confidence: 99%

“…4 A). Furthermore, accumulation of phthalides significantly decreases after bolting [ 13 ]. Expression of this gene showed a trend similar to that of synthesis and accumulation of active compounds.…”

Section: Platform Contentsmentioning

confidence: 99%

“…For instance, Peng et al [ 11 ] conducted a transcriptome analysis to explore the impact of ultraviolet B (UV-B) radiation on two different variants of A. sinensis , and Li et al [ 12 ] investigated the molecular mechanisms of flowering by comparing bolted and unbolted A. sinensis . Additionally, Feng et al [ 13 ] utilized transcriptome and metabolite profile analyses to identify 108 potential candidate isoforms associated with phthalide accumulation.…”

Section: Introductionmentioning

confidence: 99%

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ASAP: a platform for gene functional analysis in Angelica sinensis

Wu,

Da,

Xiao

et al. 2024

BMC Genomics

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Background Angelica sinensis (Danggui), a renowned medicinal orchid, has gained significant recognition for its therapeutic effects in treating a wide range of ailments. Genome information serves as a valuable resource, enabling researchers to gain a deeper understanding of gene function. In recent times, the availability of chromosome-level genomes for A. sinensis has opened up vast opportunities for exploring gene functionality. Integrating multiomics data can allow researchers to unravel the intricate mechanisms underlying gene function in A. sinensis and further enhance our knowledge of its medicinal properties. Results In this study, we utilized genomic and transcriptomic data to construct a coexpression network for A. sinensis. To annotate genes, we aligned them with sequences from various databases, such as the NR, TAIR, trEMBL, UniProt, and SwissProt databases. For GO and KEGG annotations, we employed InterProScan and GhostKOALA software. Additionally, gene families were predicted using iTAK, HMMER, OrholoFinder, and KEGG annotation. To facilitate gene functional analysis in A. sinensis, we developed a comprehensive platform that integrates genomic and transcriptomic data with processed functional annotations. The platform includes several tools, such as BLAST, GSEA, Heatmap, JBrowse, and Sequence Extraction. This integrated resource and approach will enable researchers to explore the functional aspects of genes in A. sinensis more effectively. Conclusion We developed a platform, named ASAP, to facilitate gene functional analysis in A. sinensis. ASAP (www.gzybioinformatics.cn/ASAP) offers a comprehensive collection of genome data, transcriptome resources, and analysis tools. This platform serves as a valuable resource for researchers conducting gene functional research in their projects, providing them with the necessary data and tools to enhance their studies.

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Section: Platform Contentsmentioning

confidence: 99%

Section: Platform Contentsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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ASAP: a platform for gene functional analysis in Angelica sinensis

Wu,

Da,

Xiao

et al. 2024

BMC Genomics

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“…S1) ( 19 , 20 ). However, other possible pathways for the phthalide scaffold formation could not be excluded ( 21 ), such as cyclization of 12-C fatty acid (fig. S1).…”

Section: Introductionmentioning

confidence: 99%

Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong

Nie,

Chen,

Hou

et al. 2024

Sci. Adv.

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Butylphthalide is one of the first-line drugs for ischemic stroke therapy, while no biosynthetic enzyme for butylphthalide has been reported. Here, we present a haplotype-resolved genome of Ligusticum chuanxiong , a long-cultivated and phthalide-rich medicinal plant in Apiaceae. On the basis of comprehensive screening, four Fe(II)- and 2-oxoglutarate–dependent dioxygenases and two CYPs were mined and further biochemically verified as phthalide C-4/C-5 desaturases (P4,5Ds) that effectively promoted the forming of ( S )-3- n -butylphthalide and butylidenephthalide. The substrate promiscuity and functional redundancy featured for P4,5Ds may contribute to the high phthalide diversity in L. chuanxiong . Notably, comparative genomic evidence supported L. chuanxiong as a homoploid hybrid with Ligusticum sinense as a potential parent. The two haplotypes demonstrated exceptional structure variance and diverged around 3.42 million years ago. Our study is an icebreaker for the dissection of phthalide biosynthetic pathway and reveals the hybrid origin of L. chuanxiong , which will facilitate the metabolic engineering for ( S )-3- n -butylphthalide production and breeding for L. chuanxiong .

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“…Angelica sinensis (Oliv.) Diels (Umbelliferae) (A. sinensis) is a biennial medicinal plant that thrives in cold and damp hillside areas in regions at elevated altitudes between 2200 and 3000 m [1,2]. Min County in the Gansu Province of China is the largest A. sinensis production area, accounting for 70% of China's total production [3].…”

Section: Introductionmentioning

confidence: 99%

The Dynamic Accumulation Rules of Chemical Components during the Medicine Formation Period of Angelica sinensis and Chemometric Classifying Analysis for Different Bolting Times Using ATR-FTIR

Ma,

Jiang,

et al. 2023

Molecules

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The dried roots of the perennial herb Angelica sinensis (Oliv.) Diels (AS) are commonly used as medicinal and edible resources. In commercial planting, early bolting and flowering (EB) of ca. 60% in the medicine formation period reduces root yield and quality, becoming a significant bottleneck in agricultural production. In the cultivation process, summer bolting (SB) occurs from June to July, and autumn bolting (AB) occurs in September. The AB root is often mistaken for the AS root due to its similar morphological characteristics. Few studies have involved whether the root of AB could be used as herbal medicine. This study explored and compared the accumulation dynamics of primary and secondary metabolites in AS and EB roots during the vegetative growth stage (from May to September) by light microscopy, ultraviolet spectrometry, and HPLC methods. Under a microscope, the amount of free starch granules and oil chamber in the AS root increased. On the contrary, they decreased further from EB-Jul to EB-Sep. By comparison, the wall of the xylem vessel was slightly thickened and stacked, and the cell walls of parenchyma and root cortex tissue were thickened in the EB root. Early underground bolting reduces soluble sugar, soluble protein, free amino acids, total C element, total N element, ferulic acid, and ligustilide accumulation, accompanied by the lignification of the root during the vegetative growth stage. Furthermore, a total of 55 root samples from different bolting types of AS root (29 samples), SB root (14 samples), and AB root (12 samples) were collected from Gansu Province during the harvesting period (October). The later the bolting occurred, the less difference there was between unbolted and bolted roots in terms of morphological appearance and efficacy components. Fourier transform infrared spectroscopy with the attenuated total reflection mode (ATR-FTIR) provides a “holistic” spectroscopic fingerprinting of all compositions in the tested sample. The ATR-FTIR spectrum of the AB root was similar to that of the AS root. However, the number and location of absorption peaks in the spectra of SB were different, and only one strong absorption peak at 1021 cm−1 was regarded as the characteristic peak of C-O stretching vibration in lignin. The ATR-FTIR spectra can be effectively differentiated based on their various characteristics using orthogonal partial least squares discrimination analysis (OPLS-DA). Results were assessed using multiple statistical techniques, including Spearman’s correlation, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and OPLS-DA. Among these methods, the ATR-FTIR data demonstrated the most effective outcomes in differentiating between viable and non-viable roots for their application in herbal medicine. Essential substances are ferulic acid and flavonoid, which are much more abundant in the AB root. It provides a material basis for the pharmacological action of the AB roots and a theoretical basis for improving their availability.

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Investigation of Enzymes in the Phthalide Biosynthetic Pathway in Angelica sinensis Using Integrative Metabolite Profiles and Transcriptome Analysis

Cited by 9 publications

References 40 publications

ASAP: a platform for gene functional analysis in Angelica sinensis

ASAP: a platform for gene functional analysis in Angelica sinensis

Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong

The Dynamic Accumulation Rules of Chemical Components during the Medicine Formation Period of Angelica sinensis and Chemometric Classifying Analysis for Different Bolting Times Using ATR-FTIR

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