Comparative transcriptome and metabolome analyses of four Panax species explore the dynamics of metabolite biosynthesis

Koo, Hyunjin; Lee, Yun Sun; Nguyen, Van Binh; Giang, Vo Ngoc Linh; Koo, Hyun Jo; Park, Hyun-Seung; Mohanan, Padmanaban; Song, Young Hun; Ryu, Byeol; Kang, Kyo Bin; Sung, Sang Hyun; Yang, Tae-Jin

doi:10.1016/j.jgr.2022.07.001

Cited by 7 publications

(8 citation statements)

References 59 publications

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“…The global metabolome profile of the roots of both normal and purple root color variants indicated that both have different metabolome compositions. Firstly, the presence of 11 compound classes in both types is consistent with the earlier work on the metabolome profiles of P. notoginseng in that the two are rich in health-beneficial compounds [2,24,25]. The differential accumulation of the 123 metabolites between the two types of roots with different colors indicates that both can offer variable contents of a range of compounds.…”

Section: Discussionsupporting

confidence: 86%

“…The differential accumulation of the 123 metabolites between the two types of roots with different colors indicates that both can offer variable contents of a range of compounds. Earlier works have shown that Panax species differ in their metabolomic profiles [25,26]. Within one species, the different tissues of the same plant can also offer variations in the contents of a range of compounds [27].…”

Section: Discussionmentioning

confidence: 99%

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Combined Metabolome and Transcriptome Analysis of Creamy Yellow and Purple Colored Panax notoginseng Roots

He,

Zhang,

Huo

et al. 2023

Life

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Panax notoginseng (Burk.) F.H. Chen is a species of the Araliaceae family that inhabits southwestern China, Burma, and Nepal. It is cultivated on a commercial scale in Yunnan province, China, owing to its significance in traditional Chinese medicine. Panax notoginseng roots are usually yellow-white (HS); however, purple roots (ZS) have also been reported. The majority of P. notoginseng research has concentrated on the identification and production of natural chemicals in HS; however, there is little to no information about the composition of ZS. Using UPLC-MS/MS, we investigated the global metabolome profile of both ZS- and HS-type roots and discovered 834 metabolites from 11 chemical groups. There were 123 differentially accumulated metabolites (DAM) in the HS and ZS roots, which were classified as lipids and lipid-like molecules, polyketides, organoheterocyclic chemicals, and organooxygen compounds. We investigated the associated compounds in the DAMs because of the importance of anthocyanins in color and saponins and ginsenosides in health benefits. In general, we discovered that pigment compounds such as petunidin 3-glucoside, delphinidin 3-glucoside, and peonidin-3-O-beta-galactoside were more abundant in ZS. The saponin (eight compounds) and ginsenoside (26 compounds) content of the two varieties of roots differed as well. Transcriptome sequencing revealed that flavonoid and anthocyanin production genes were more abundant in ZS than in HS. Similarly, we found differences in gene expression in genes involved in terpenoid production and related pathways. Overall, these findings suggest that the purple roots of P. notoginseng contain varying amounts of ginsenosides and anthocyanins compared to roots with a creamy yellow color.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Combined Metabolome and Transcriptome Analysis of Creamy Yellow and Purple Colored Panax notoginseng Roots

He,

Zhang,

Huo

et al. 2023

Life

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“…Such a large-scale multiomics study regarding Panax species has not yet been reported. However, small-scale studies integrating transcriptome and ginsenoside profiles were recently conducted and provided many insights into ginsenoside biosynthesis [ [83] , [84] , [85] , [86] , [87] ], the tissue-level distributions of ginsenosides and their biosynthesis [ 88 , 89 ], and the effects of microorganisms [ 90 , 91 ]. We anticipate that further multiomics studies with Panax species will be conducted in the near future.…”

Section: Perspective and Conclusionmentioning

confidence: 99%

Mass spectrometry-based ginsenoside profiling: Recent applications, limitations, and perspectives

Kim,

Ryu

et al. 2024

Journal of Ginseng Research

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“…It is of a great significance to characterize genes related in secondary metabolite biosynthesis between closely related species or varieties in medicinal plants ( Koo et al., 2022 ; Liu et al., 2022 ; Shafi et al., 2022 ), or between different tissues in same species ( He et al., 2022a ; Naika et al., 2022 ). The comparative transcriptome analysis of the marijuana strain Purple Kush and the ‘Finola’ cultivar of Cannabis sativa demonstrated that the Δ9-tetrahydrocannabinolic acid synthase was detected in Purple Kush but replaced by cannabidiolic acid synthase in the ‘Finola’ cultivar, explaining the significant chemical difference between marijuana-derived Δ9-tetrahydrocannabinol (THC) and hemp-derived cannabidiol (CBD) ( van Bakel et al., 2011 ).…”

Section: Functional Gene Mining Of Medicinal Plant Transcriptome To C...mentioning

confidence: 99%

Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery

Zhang

Zhou²,

Meng³

et al. 2023

Front. Plant Sci.

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Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world’s demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs’ phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.

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Comparative transcriptome and metabolome analyses of four Panax species explore the dynamics of metabolite biosynthesis

Cited by 7 publications

References 59 publications

Combined Metabolome and Transcriptome Analysis of Creamy Yellow and Purple Colored Panax notoginseng Roots

Combined Metabolome and Transcriptome Analysis of Creamy Yellow and Purple Colored Panax notoginseng Roots

Mass spectrometry-based ginsenoside profiling: Recent applications, limitations, and perspectives

Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery

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