Transcriptome and Metabolome Analyses of the Flowers and Leaves of Chrysanthemum dichrum

Integrating Physiology, Transcriptome, and Metabolomics Reveals the Potential Mechanism of Nitric Oxide Concentration-Dependent Regulation of Embryo Germination in Sorbus pohuashanensis

Nitric oxide (NO) breaks a seed's dormancy and stimulates germination by signaling. However, the key physiological metabolic pathways and molecular regulatory mechanisms are still unclear. Therefore, this study used physiological, transcriptomic, and metabolomics methods to analyze the key genes and metabolites involved in the NO regulation of plant embryo germination and their potential regulatory mechanisms. The physiological analysis results indicate that the appropriate concentration of NO increased the content of NO and hydrogen peroxide (H2O2) in cells, stimulated the synthesis of ethylene and jasmonic acid (JA), induced a decrease in abscisic acid (ABA) content, antagonistic to the gibberellin (GA3) effect, and promoted embryo germination and subsequent seedling growth. However, the high concentrations of NO caused excessive accumulation of H2O2, destroyed the reactive oxygen species (ROS) balance, and inhibited embryo germination and seedling growth. The combined analysis of transcriptomics and metabolomics showed that the genes related to phenylpropanoid (phenylalanine ammonia-lyase, trans-cinnamate 4-monooxygenase, ferulate-5-hydroxylase, coniferyl-alcohol glucosyltransferase), and flavonoid synthesis (10 genes such as CHS) were significantly up-regulated during embryo germination. The high concentration of exogenous NO inhibited embryo germination by up-regulating the expression of 4-coumaric acid coenzyme A ligase (4CL) and negatively regulating the expression of flavonoid synthesis genes. This suggests that NO concentration-dependently regulates phenylpropanoid and flavonoid biosynthesis, thereby affecting ROS metabolism and hormone levels, and ultimately regulates the dormancy and germination of Sorbus pohuashanensis embryos.

Targeted Metabolites and Transcriptome Analysis Uncover the Putative Role of Auxin in Floral Sex Determination in Litchi chinensis Sonn

Litchi exhibits a large number of flowers, many flowering batches, and an inconsistent ratio of male and female flowers, frequently leading to a low fruit-setting rate. Floral sexual differentiation is a crucial phase in perennial trees to ensure optimal fruit production. However, the mechanism behind floral differentiation remains unclear. The objective of the study was to identify the role of auxin in floral differentiation at the transcriptional level. The results showed that the ratio of female flowers treated with naphthalene acetic acid (NAA) was significantly lower than that of the control stage (M0/F0). The levels of endogenous auxin and auxin metabolites were measured in male and female flowers at different stages of development. It was found that the levels of IAA, IAA-Glu, IAA-Asp, and IAA-Ala were significantly higher in male flowers compared to female flowers. Next-generation sequencing and modeling were employed to perform an in-depth transcriptome analysis on all flower buds in litchi 'Feizixiao' cultivars (Litchi chinensis Sonn.). Plant hormones were found to exert a significant impact on the litchi flowering process and flower proliferation. Specifically, a majority of differentially expressed genes (DEGs) related to the auxin pathway were noticeably increased during male flower bud differentiation. The current findings will enhance our comprehension of the process and control mechanism of litchi floral sexual differentiation. It also offers a theoretical foundation for implementing strategies to regulate flowering and enhance fruit production in litchi cultivation.

Comparative Analysis of the Chemical Constituents of Chrysanthemum morifolium with Different Drying Processes Integrating LC/GC-MS-Based, Non-Targeted Metabolomics

Chrysanthemum morifolium is a perennial herbaceous plant in the Asteraceae family that is used as a medicine and food owing to its superior pharmacological properties. Irrespective of its application, C. morifolium must be dried before use. Shade drying (YG) and heat drying (HG) are the two drying methods used in most origins. Given the abundance of flavonoids, phenolic acids, and terpenoids, the primary medicinal active constituents of C. morifolium, it is important to determine whether the composition and content of these compounds are altered during the drying processes. To test this, the changes in the chemical composition of C. morifolium flowers after YG and HG using full-spectrum, non-targeted LC/GC-MS-based metabolomics and, subsequently, the three indicator components of C. morifolium-chlorogenic acid, 3,5-dicaffeoylquinic acid, and luteolin-7-O-glucoside-were accurately quantified by HPLC. The results of the non-targeted metabolomics analysis revealed that YG- and HG-processed C. morifolium differed significantly with respect to chemical contents, especially flavonoids, phenolic acids, and terpenoids. The levels of the indicator components and their precursors also differed significantly between the YG and HG treatments. The contents of most of the flavonoids and key phenolic acids, terpenoids, and carbohydrates were higher with YG than with HG pre-treatment. These results revealed the changes in the chemical composition of C. morifolium during the YG and HG processes, thus providing a reference for the further optimization of the production and processing of chrysanthemums.

Integrative transcriptomic and metabolomic analyses reveal the phenylpropanoid and flavonoid biosynthesis of Prunus mume

Prunus mume is an important medicinal plant with ornamental and edible value. Its flowers contain phenylpropanoids, flavonoids and other active components, that have important medicinal and edible value, yet their molecular regulatory mechanisms in P. mume remain unclear. In this study, the content of total flavonoid and total phenylpropanoid of P. mume at different developmental periods was measured first, and the results showed that the content of total flavonoid and total phenylpropanoid gradually decreased in three developmental periods. Then, an integrated analysis of transcriptome and metabolome was conducted on three developmental periods of P. mume to investigate the law of synthetic accumulation for P. mume metabolites, and the key enzyme genes for the biosynthesis of phenylpropanoids and flavonoids were screened out according to the differentially expressed genes (DEGs). A total of 14,332 DEGs and 38 differentially accumulate metabolites (DAMs) were obtained by transcriptomics and metabolomics analysis. The key enzyme genes and metabolites in the bud (HL) were significantly different from those in the half-opening (BK) and full-opening (QK) periods. In the phenylpropanoid and flavonoid biosynthesis pathway, the ion abundance of chlorogenic acid, naringenin, kaempferol, isoquercitrin, rutin and other metabolites decreased with the development of flowers, while the ion abundance of cinnamic acid increased. Key enzyme genes such as HCT, CCR, COMT, CHS, F3H, and FLS positively regulate the downstream metabolites, while PAL, C4H, and 4CL negatively regulate the downstream metabolites. Moreover, the key genes FLS (CL4312-2, CL4312-3, CL4312-4, CL4312-5, CL4312-6) regulating the synthesis of flavonols are highly expressed in bud samples. The dynamic changes of these metabolites were validated by determining the content of 14 phenylpropanoids and flavonoids in P. mume at different developmental periods, and the transcription expression levels of these genes were validated by real-time PCR. Our study provides new insights into the molecular mechanism of phenylpropanoid and flavonoid accumulation in P. mume.

Pathogen-triggered metabolic adjustments to potato virus Y infection in potato

Potato (Solanum tuberosum L) is affected by several viral pathogens with the most economically damaging being potato virus Y (PVY). At least nine biologically distinct variants of PVY are known to attack potato, with necrotic types named PVYNTN and PVYN-Wi being the most recent additions to the list. So far, the molecular plant-virus interactions underlying this pathogenicity are not fully understood. In this study, gas chromatography coupled with mass spectroscopy (GC-MS) was used for an untargeted investigation of the changes in leaf metabolomes of PVY-resistant cultivar Premier Russet, and a susceptible cultivar, Russet Burbank, following inoculation with three PVY strains, PVYNTN, PVYN-Wi, and PVYO. Analysis of the resulting GC-MS spectra with the online software Metaboanalyst (version 5.0) uncovered several common and strain-specific metabolites that are induced by PVY inoculation. In Premier Russet, the major overlap in differential accumulation was found between PVYN-Wi and PVYO. However, the 14 significant pathways occurred solely due to PVYN-Wi. In contrast, the main overlap in differential metabolite profiles and pathways in Russet Burbank was between PVYNTN and PVYO. Overall, limited overlap was observed between PVYNTN and PVYN-Wi. As a result, PVYN-Wi-induced necrosis may be mechanistically distinguishable from that of PVYNTN. Furthermore, 10 common and seven cultivar-specific metabolites as potential indicators of PVY infection and susceptibility/resistance were identified by using PLS-DA and ANOVA. In Russet Burbank, glucose-6-phosphate and fructose-6-phosphate were particularly affected by strain-time interaction. This highlights the relevance of the regulation of carbohydrate metabolism for defense against PVY. Some strain- and cultivar-dependent metabolite changes were also observed, reflecting the known genetic resistance-susceptibility dichotomy between the two cultivars. Consequently, engineering broad-spectrum resistance may be the most effective breeding strategy for managing these necrotic strains of PVY.

The genus Chrysanthemum: Phylogeny, biodiversity, phytometabolites, and chemodiversity

The ecologically and economically important genus Chrysanthemum contains around 40 species and many hybrids and cultivars. The dried capitulum of Chrysanthemum morifolium (CM) Ramat. Tzvel, i.e., Flos Chrysanthemi, is frequently used in traditional Chinese medicine (TCM) and folk medicine for at least 2,200 years. It has also been a popular tea beverage for about 2,000 years since Han Dynasty in China. However, the origin of different cultivars of CM and the phylogenetic relationship between Chrysanthemum and related Asteraceae genera are still elusive, and there is a lack of comprehensive review about the association between biodiversity and chemodiversity of Chrysanthemum. This article aims to provide a synthetic summary of the phylogeny, biodiversity, phytometabolites and chemodiversity of Chrysanthemum and related taxonomic groups, focusing on CM and its wild relatives. Based on extensive literature review and in light of the medicinal value of chrysanthemum, we give some suggestions for its relationship with some genera/species and future applications. Mining chemodiversity from biodiversity of Chrysanthemum containing subtribe Artemisiinae, as well as mining therapeutic efficacy and other utilities from chemodiversity/biodiversity, is closely related with sustainable conservation and utilization of Artemisiinae resources. There were eight main cultivars of Flos Chrysanthemi, i.e., Hangju, Boju, Gongju, Chuju, Huaiju, Jiju, Chuanju and Qiju, which differ in geographical origins and processing methods. Different CM cultivars originated from various hybridizations between multiple wild species. They mainly contained volatile oils, triterpenes, flavonoids, phenolic acids, polysaccharides, amino acids and other phytometabolites, which have the activities of antimicrobial, anti-viral, antioxidant, anti-aging, anticancer, anti-inflammatory, and closely related taxonomic groups could also be useful as food, medicine and tea. Despite some progresses, the genetic/chemical relationships among varieties, species and relevant genera have yet to be clarified; therefore, the roles of pharmacophylogeny and omics technology are highlighted.