Research Progress of Genomics Applications in Secondary Metabolites of Medicinal Plants: A Case Study in Safflower

Abstract

Medicinal plants, recognized as significant natural resources, have gained prominence in response to the increasing global demand for herbal medicines, necessitating the large-scale production of these plants and their derivatives. Medicinal plants are exposed to a variety of internal and external factors that interact to influence the biosynthesis and accumulation of secondary metabolites. With the rapid development of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics, multi-omics technologies have become important tools for revealing the complexity and functionality of organisms. They are conducive to further uncovering the biological activities of secondary metabolites in medicinal plants and clarifying the molecular mechanisms underlying the production of secondary metabolites. Also, artificial intelligence (AI) technology accelerates the comprehensive utilization of high-dimensional datasets and offers transformative potential for multi-omics analysis. However, there is currently no systematic review summarizing the genomic mechanisms of secondary metabolite biosynthesis in medicinal plants. Safflower (Carthamus tinctorius L.) has rich and diverse bioactive flavonoids, among of which Hydroxysafflor yellow A (HSYA) is specific to safflower and emerging as a potential medication for treating a wide range of diseases. Hence, significant progress has been made in the study of safflower as an excellent example for the regulation of secondary metabolites in medicinal plants in recent years. Here, we review the progress on the understanding of the regulation of main secondary metabolites at the multi-omics level, and summarize the influence of various factors on their types and contents, with a particular focus on safflower flavonoids. This review aims to provide a comprehensive insight into the regulatory mechanisms of secondary metabolite biosynthesis from the perspective of genomics.

Keywords: genomics; medicinal plants; regulation; safflower; secondary metabolites.

Figure 3

Development of genomic technologies for medicinal plants [93,101,102,103,104,105,106,107].

Figure 4

Overview of multi-omics technology [88,126,127,128,129,130,131].

Figure 5

Regulation mechanism of secondary metabolites in safflower [149]. The red-shaded box represents the methods of omics technologies, the grey-shaded box represents the impact of environmental factors on safflower, and the yellow-shaded box represents the biosynthetic pathway of flavonoids in safflower. Note: The enzyme names are abbreviated as follows: PAL, phenylalanine ammonia lyase; C4H, cinnamic acid 4-hydroxylase; 4CL, 4-coumarate: CoA ligase; CHS, chalcone synthase; UGT, UDP-glycosyltransferase; P450, cytochrome P450; IFS, isoflavone synthase; POD, peroxidase; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; F3′H, flavanone 3′-hydroxylase; F3′5′H, flavanone 3′,5′-hydroxylase; DFR, dihydroflavonol 4-reductase; ANS, anthocyanidin synthase; OMT, O-methyl transferases; FLS, flavonol synthase; LAR, leucoanthocyanidin reductase; ANR, anthocyanidin reductase; FG2, flavonol-3-O-glucoside L-rhamnosyltransferase.

Figure 1

Number of articles published on genomic research of medicinal plants over the past 10 years. (a) Statistics of the number of publications by year. (b) Statistics of the number of publications by country. The visualization was generated using R (version 4.4.1) with the ggplot2 (version 3.5.1), dplyr (version 1.1.4), and cowplot (version 1.1.3) packages.

Figure 2

Common secondary metabolites and their medicinal values. The blue-shaded box represents alkaloids, the gray-shaded box represents terpenoids, the yellow-shaded box represents flavonoids, and the pink-shaded box represents quinones. The figure was created using Adobe Illustrator 2022.