Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

Shen, Tengfei; Zheng, Yanhui; Liu, Qian; Chen, Caihui; Huang, Lili; Deng, Shaozhi; Xu, Meng; Yang, Chunxia

doi:10.3390/ijms23116321

Cited by 7 publications

(5 citation statements)

References 59 publications

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“…The high expression of G8Os in the kernel of Zhizi might be the reason for the high content of geniposide in the kernel ( Pan et al., 2021 ). Recently, there have been many studies on the metabolic pathway of crocin biosynthesis in Zhizi ( Xu et al., 2020a ; Shen et al., 2022 ). During the development of gardenia fruit, when the fruit color turns red, key enzyme genes involved in the biosynthesis of crocin exhibit significantly high expression levels ( Zhang et al., 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive quality evaluation of different types of Gardeniae Fructus (Zhizi) and Shuizhizi based on LC-MS/MS

Qian,

Hu,

Wang

et al. 2024

Front. Plant Sci.

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Gardeniae Fructus (Zhizi) serves as both a medicinal and edible substance and finds widespread use in various industries. There are often two kinds of medicinal materials in the market: Zhizi and Shuizhizi. Typically, Zhizi with small, round fruit is used for medicinal purposes, while Shuizhizi, characterized by large, elongated fruit, is employed for dyeing. Market surveys have revealed a diverse range of Zhizi types, and modern research indicates that Shuizhizi contains rich chemical components and pharmacological activities. In this study, we collected 25 batches of Zhizi and Shuizhizi samples, categorizing them based on appearance into obovate and round fruits, with seven length grades (A–G). Using the ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-QQQ-MS/MS) method, we simultaneously quantified 13 main chemical components in fruits of Gardenia species. In addition, we compared the weight percentage of the pericarp, flesh, and seeds parts of samples with different traits, and quantified 13 chemical components in different parts. Results indicated that, aside from a few instances of overlapping fruit size ranges, Shuizhizi generally exhibits larger and longer dimensions than Zhizi. The weight proportion of the Shuizhizi pericarp is often higher than that of the Zhizi pericarp. Quantitative results highlighted significant differences in the chemical component content between Zhizi and Shuizhizi, with Shuizhizi generally containing higher levels of iridoids. The PCA and OPLS-DA analysis distinctly divided Shuizhizi and Zhizi, among which three iridoids, two organic acids, and one flavonoid made significant contributions to their classification. Cluster heatmap analysis also demonstrated complete separation between Zhizi and Shuizhizi, with clear distinctions among Zhizi samples from different origins. The distribution of the 13 chemical components in different Zhizi and Shuizhizi parts remained consistent, with iridoids and pigments concentrated in the seeds and flesh, and two organic acids and one flavonoid enriched in the pericarp. In summary, this study contributes valuable insights for classifying Zhizi and offers guidance on the rational use of Shuizhizi and the different parts of Zhizi.

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Section: Discussionmentioning

confidence: 99%

Comprehensive quality evaluation of different types of Gardeniae Fructus (Zhizi) and Shuizhizi based on LC-MS/MS

Qian,

Hu,

Wang

et al. 2024

Front. Plant Sci.

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“…One of the important synthetic precursors of crocin is carotenoid. It is reported that carotenoid biosynthesis pathway has a great influence on the synthesis of crocin in gardenia ( Shen et al, 2022 ), and 30 DEGs have been annotated on the carotenoid biosynthesis KEGG pathway of gardenia ( Pan et al, 2021 ). In addition to carotenoid biosynthesis pathway, flavonoid biosynthesis (ko00941) and flavone and flavonol biosynthesis (ko00944) are important secondary metabolites that exist widely in plants, which not only play an important role in plant growth and development, but also have outstanding applications in food and medicine.…”

Section: Discussionmentioning

confidence: 99%

“…The chemical components of gardenia fruits are mainly iridoids, including geniposide and gardenic acid, among which geniposide is one of the most active components ( Long et al, 2013 ; Xu et al, 2016 ; Zhou et al, 2021 ). In addition, gardenia also contains carotenoid compounds, such as crocin, which can regulate the neural center, improve memory and cognition ( Tian et al, 2020 ; Shen et al., 2022 ), and phenolic acid compounds, mainly chlorogenic acid, which can lower blood pressure, antioxidant, free radical scavenging and regulate the body’s immunity ( Liu et al, 2020 ). With the continuous research, development and utilization, gardenia has become the first batch of edible and medicinal plants in China.…”

Section: Introductionmentioning

confidence: 99%

Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides

Xu,

Chen,

Zhang

et al. 2023

PeerJ

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Background Gardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough. Methods In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.

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“…Recent studies have correlated long noncoding RNAs (lncRNAs) with terpene synthesis in angiosperms, such as Citrus limon (Bordoloi et al, 2022), Gardenia jasminoides (Shen et al, 2022), and Zanthoxylum armatum (Liu et al, 2022), and gymnosperms, such as Ginkgo bioloba (Han X et al, 2021) and Pinus massoniana (Feng et al, 2022). A previous study reported that lncRNAs regulate cineole, linalool, and nerolidol biosynthesis in C. camphora (Ni et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Full-length transcriptome sequencing reveals the molecular mechanism of monoterpene and sesquiterpene biosynthesis in Cinnamomum burmannii

Hou

Zhang²,

Xie³

et al. 2023

Front. Genet.

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Essential oil of Cinnamomum burmannii is rich in monoterpenes and sesquiterpenes and is widely used in cosmetics and medicines. Knowledge about the enzymes that catalyze the formation of monoterpenes and sesquiterpenes in C. burmannii is insufficient. Therefore, anatomy observation of C. burmannii at the four developmental stages (7 days, CBS1; 14 days, CBS2; 21 days, CBS3, and 28 days, CBS4) were conducted to elucidate the origins of essential oil production. Twelve full-length transcriptomes of C. burmannii leaves at the four stages were generated using Oxford Nanopore Technologies. GC-MS analysis revealed 15 monoterpene and sesquiterpenes dramatically increased from CBS1 to CBS4. A weighted correlation network analysis (WGCNA) in association and differentially expressed genes across four developmental stages were performed. A total of 44 differentially expressed genes (DEGs) were involved in terpenoid syntheses during leaf development. Among them, the DEGs of the mevalonate acid (MVA) pathway were predominantly expressed at CBS1, while those of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway showed increased expression from CBS2 to CBS4. Besides, fourteen genes were associated with monoterpene synthesis and nine with sesquiterpene synthesis. Functions of these DEGs were further predicted with regard to gene expression profile and phylogenetic relationship with those characterized in previous studies. In addition, 922 long noncoding RNAs (lncRNAs) were detected, of which twelve were predicted to regulate monoterpene and sesquiterpene biosynthesis. The present study provided new insights the molecular mechanisms of monoterpenoid and sesquiterpenoid syntheses of C. burmannii.

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Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

Cited by 7 publications

References 59 publications

Comprehensive quality evaluation of different types of Gardeniae Fructus (Zhizi) and Shuizhizi based on LC-MS/MS

Comprehensive quality evaluation of different types of Gardeniae Fructus (Zhizi) and Shuizhizi based on LC-MS/MS

Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides

Full-length transcriptome sequencing reveals the molecular mechanism of monoterpene and sesquiterpene biosynthesis in Cinnamomum burmannii

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