Transcriptome and Metabolome Analyses Reveal Differences in Terpenoid and Flavonoid Biosynthesis in Cryptomeria fortunei Needles Across Different Seasons

Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats

Soybean has outstanding nutritional and medicinal value because of its abundant protein, oil, and flavonoid contents. This crop has rich seed coat colors, such as yellow, green, black, brown, and red, as well as bicolor variants. However, there are limited reports on the synthesis of flavonoids in the soybean seed coats of different colors. Thus, the seed coat metabolomes and transcriptomes of five soybean germplasms with yellow (S141), red (S26), brown (S62), green (S100), and black (S124) seed coats were measured. In this study, 1645 metabolites were detected in the soybean seed coat, including 426 flavonoid compounds. The flavonoids differed among the different-colored seed coats of soybean germplasms, and flavonoids were distributed in all varieties. Procyanidins A1, B1, B6, C1, and B2, cyanidin 3-O-(6″-malonyl-arabinoside), petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, and malvidin 3-laminaribioside were significantly upregulated in S26_vs._S141, S62_vs._S141, S100_vs._S141, and S124_vs._S141 groups, with a variation of 1.43-2.97 × 1013 in terms of fold. The differences in the contents of cyanidin 3-O-(6″-malonyl-arabinoside) and proanthocyanidin A1 relate to the seed coat color differences of red soybean. Malvidin 3-laminaribioside, petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, cyanidin 3-O-(6″-malonyl-arabinoside), and proanthocyanidin A1 affect the color of black soybean. The difference in the contents of procyanidin B1 and malvidin 3-glucoside-4-vinylphenol might be related to the seed coat color differences of brown soybeans. Cyanidin 3-gentiobioside affects the color of green soybean. The metabolomic-transcriptomic combined analysis showed that flavonoid biosynthesis is the key synthesis pathway for soybean seed color formation. Transcriptome analysis revealed that the upregulation of most flavonoid biosynthesis genes was observed in all groups, except for S62_vs._S141, and promoted flavonoid accumulation. Furthermore, CHS, CHI, DFR, FG3, ANR, FLS, LAR, and UGT88F4 exhibited differential expression in all groups. This study broadens our understanding of the metabolic and transcriptomic changes in soybean seed coats of different colors and provides new insights into developing bioactive substances from soybean seed coats.

Essential Oil Composition and Anti-Cholinesterase Properties of Cryptomeria japonica Foliage Harvested in São Miguel Island (Azores) in Two Different Seasons

The Azorean Cryptomeria japonica forest operations and wood industry generate considerable foliage biomass residues that are used for local essential oil (EO) production. However, research on seasonal variation of C. japonica EO remains scarce. In this study, the EOs from fresh Azorean C. japonica foliage (Az-CJF) collected in autumn (Aut) and spring (Spr) were obtained via hydrodistillation and investigated for their physical properties, yield, chemical composition, and bioactivities. Both EOs presented a strong odor, a yellowish color, a density around 0.9 g·mL-1, and similar yields (approximately 1% v/w, dry matter). Nevertheless, the GC-MS analyses showed a decrease in monoterpene hydrocarbons (MH) and an increase in oxygenated sesquiterpenes (OS) contents in Spr-EO compared with Aut-EO (16% vs. 35% for MH and 45% vs. 31% for OS, respectively). In addition, the predominant components were kaur-16-ene (23%) for Spr-EO and phyllocladene (19%) for Aut-EO, revealing that both EOs were rich in diterpene hydrocarbons (29% vs. 26%). Concerning its toxicity against brine shrimp, a low mortality (0-38%) was observed at a concentration range of 100-180 μg·mL-1. Regarding the anti-cholinesterase properties, both EOs were inactive against acetylcholinesterase but showed anti-butyrylcholinesterase activity superior to (-)-α-pinene, a major compound of Az-CJF EO (IC50 values: 84, 148, and 648 μg·mL-1 for Spr-EO, Aut-EO, and α-pinene, respectively). Overall, the results indicate the potential benefit of both seasonal EOs in Alzheimer's disease treatment. In conclusion, this study demonstrated that season strongly influences the Az-CJF EO quantitative composition and thus its bioactivity, aiding in the selection of the most high-quality raw materials for use in Azorean C. japonica EO aromatherapy industry.

Integrative analysis of the transcriptome and metabolome provides insights into polysaccharide accumulation in Polygonatum odoratum (Mill.) Druce rhizome

Background

Polygonatum odoratum (Mill.) Druce is a traditional Chinese herb that is widely cultivated in China. Polysaccharides are the major bioactive components in rhizome of P. odoratum and have many important biological functions.

Methods

To better understand the regulatory mechanisms of polysaccharide accumulation in P. odoratum rhizomes, the rhizomes of two P. odoratum cultivars 'Y10' and 'Y11' with distinct differences in polysaccharide content were used for transcriptome and metabolome analyses, and the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were identified.

Results

A total of 14,194 differentially expressed genes (DEGs) were identified, of which 6,689 DEGs were down-regulated in 'Y10' compared with those in 'Y11'. KEGG enrichment analysis of the down-regulated DEGs revealed a significant enrichment of 'starch and sucrose metabolism', and 'amino sugar and nucleotide sugar metabolism'. Meanwhile, 80 differentially accumulated metabolites (DAMs) were detected, of which 52 were significantly up-regulated in 'Y11' compared to those in 'Y10'. The up-regulated DAMs were significantly enriched in 'tropane, piperidine and pyridine alkaloid biosynthesis', 'pentose phosphate pathway' and 'ABC transporters'. The integrated metabolomic and transcriptomic analysis have revealed that four DAMs, glucose, beta-D-fructose 6-phosphate, maltose and 3-beta-D-galactosyl-sn-glycerol were significantly enriched for polysaccharide accumulation, which may be regulated by 17 DEGs, including UTP-glucose-1-phosphate uridylyltransferase (UGP2), hexokinase (HK), sucrose synthase (SUS), and UDP-glucose 6-dehydrogenase (UGDH). Furthermore, 8 DEGs (sacA, HK, scrK, GPI) were identified as candidate genes for the accumulation of glucose and beta-D-fructose 6-phosphate in the proposed polysaccharide biosynthetic pathways, and these two metabolites were significantly associated with the expression levels of 13 transcription factors including C3H, FAR1, bHLH and ERF. This study provided comprehensive information on polysaccharide accumulation and laid the foundation for elucidating the molecular mechanisms of medicinal quality formation in P. odoratum rhizomes.

Transcriptome analysis revealed the role of moderate exogenous methyl jasmonate treatments in enhancing the metabolic pathway of L-borneol in the Blumea balsamifera

Introduction

Blumea balsamifera L. (Ainaxiang) DC. is a perennial herb of the compositae family. It is also the primary source of natural borneol. Endo-borneol, the principal medical active element in B. balsamifera, is anti-inflammatory, antioxidant, and analgesic; enhances medicine absorption; refreshes; and is used as a spice and in cosmetic. Industrialization of B. balsamifera is limited by its low L-borneol concentration. Thus, understanding the accumulation pattern of the secondary metabolite endo-borneol and its synthesis process in secondary metabolism is critical for increasing B. balsamifera active ingredient content and cultivation efficiency.

Methods

In this work, B. balsamifera was treated with varying concentrations (1.00 and 10.00 mmol/L) of methyl jasmonate (MeJA) as an exogenous foliar activator. The physiological parameters and L-borneol concentration were then assessed. Transcriptome sequencing of B. balsamifera-induced leaves was used to identify key genes for monoterpene synthesis.

Results

The treatment effect of 1 mmol/L MeJA was the best, and the leaves of all three leaf positions accumulated the highest L-borneol after 120 h, correspondingly 3.043 mg·g-1 FW, 3.346 mg·g-1 FW, and 2.044 mg·g-1 FW, with significant differences from the control. The main assembly produced 509,285 transcripts with min and max lengths of 201 and 23,172, respectively. DEG analysis employing volcano blots revealed 593, 224, 612, 2,405, 1,353, and 921 upregulated genes and 4, 123, 573, 1,745, 766, and 763 downregulated genes in the treatments D1_1vsCK, D1_10vsCK, D2_1vsCK, D2_10vsCK, D5_1vsCK, and D5_10vsCK. Interestingly, when exposed to MeJA treatments, the MEP pathway's unigenes express themselves more than those of the MVA route. Finally, when treated with 1 mmol/L, the genes DXR, DXS, and GPS showed increased expression over time. At the same time, a 10 mmol/L therapy resulted in elevated levels of ispH and GGPS.

Discussion

Our preliminary research indicates that exogenous phytohormones can raise the level of L borneol in B. balsamifera (L.) DC when given in the appropriate amounts. The most significant discovery made while analyzing the effects of different hormones and concentrations on B. balsamifera (L.) DC was the effect of 1 mmol/L MeJA treatment.

Soil Application of Bacillus subtilis Regulates Flavonoid and Alkaloids Biosynthesis in Mulberry Leaves

Flavonoids and alkaloids are the major active ingredients in mulberry leaves that have outstanding medicinal value. Bacillus subtilis can effectively activate the plants defense response and regulate the plant secondary metabolism. In this study, we explored the effects of soil application of B. subtilis on the content of flavonoids and the most important alkaloids (1-deoxynojirimycin, DNJ) in mulberry leaves. Significant decreases in flavonoid content were observed in tender leaves and mature leaves after treatment with B. subtilis; at the same time, significant increases in DNJ content were observed in tender leaves. Based on widely targeted LC-MS/MS and high-throughput approaches, we screened out 904 differentially synthesized metabolites (DSMs) and 9715 differentially expressed genes (DEGs). KEGG analyses showed that these DSMs and DEGs were both significantly enriched in the biosynthesis of secondary metabolites, flavonoid synthesis and plant hormone signal transduction. Further correlation analysis of DEMs and DEGs showed that 40 key genes were involved in flavonoid biosynthesis, with 6 key genes involved in DNJ biosynthesis. The expression of CHS, CHI, F3H, F3'H, FLS, UGT and AOC significantly responded to B. subtilis soil application. This study broadens our understanding of the molecular mechanisms underlying the accumulation of flavonoids and alkaloids in mulberry leaves.

Potential Regulatory Networks and Heterosis for Flavonoid and Terpenoid Contents in Pak Choi: Metabolomic and Transcriptome Analyses

Pak choi exhibits a diverse color range and serves as a rich source of flavonoids and terpenoids. However, the mechanisms underlying the heterosis and coordinated regulation of these compounds-particularly isorhamnetin-remain unclear. This study involved three hybrid combinations and the detection of 528 metabolites from all combinations, including 26 flavonoids and 88 terpenoids, through untargeted metabolomics. Analysis of differential metabolites indicated that the heterosis for the flavonoid and terpenoid contents was parent-dependent, and positive heterosis was observed for isorhamnetin in the two hybrid combinations (SZQ, 002 and HMG, ZMG). Moreover, there was a high transcription level of flavone 3'-O-methyltransferase, which is involved in isorhamnetin biosynthesis. The third group was considered the ideal hybrid combination for investigating the heterosis of flavonoid and terpenoid contents. Transcriptome analysis identified a total of 12,652 DEGs (TPM > 1) in various groups that were used for comparison, and DEGs encoding enzymes involved in various categories, including "carotenoid bio-synthesis" and "anthocyanin biosynthesis", were enriched in the hybrid combination (SZQ, 002). Moreover, the category of anthocyanin biosynthesis also was enriched in the hybrid combination (HMG, ZMG). The flavonoid pathway demonstrated more differential metabolites than the terpenoid pathway did. The WGCNA demonstrated notable positive correlations between the dark-green modules and many flavonoids and terpenoids. Moreover, there were 23 ERF genes in the co-expression network (r ≥ 0.90 and p < 0.05). Thus, ERF genes may play a significant role in regulating flavonoid and terpenoid biosynthesis. These findings enhance our understanding of the heterosis and coordinated regulation of flavonoid and terpenoid biosynthesis in pak choi, offering insights for genomics-based breeding improvements.