RNA-Seq reveals the key pathways and genes involved in the light-regulated flavonoids biosynthesis in mango (Mangifera indica L.) peel

Integrated transcriptomics and lipidomics reveal mechanisms regulating lipids formation and accumulation in oil body during walnut seed development

BACKGROUND

Through combined analysis of the transcriptomics and lipidomics of walnut, the possible molecular mechanism of lipid formation and accumulation in oil bodies was revealed.

CONCLUSION

The formation and accumulation of lipids are critical determinants of nut quality, with walnut storing lipids primarily in oil bodies (OBs). Currently, there is still a lack of systematic research on the formation and accumulation of lipids in walnut OBs (WOBs). Therefore, this study integrated lipidomics and transcriptomics to comprehensively identify the changes in WOBs and walnut kernels at 60, 74, 88, 102, 116, and 130 days after pollination (DAP). The results showed that fatty acid content in walnut kernels and WOBs had opposite trends, especially oleic, linoleic, and linolenic. Principal component analysis of the samples and cluster analysis of differentially expressed genes (DEGs) showed that the total samples were divided into three main groups: 60-74, 88-102, and 116-130 DAP. RNA sequencing generated 33,918 unigenes (14,995 DEGs), including 228 DEGs highly related to lipid metabolism, in 18 cDNA libraries prepared from walnut kernel. These genes were mainly involved in metabolic pathways such as pyruvate metabolism, glycerophospholipid metabolism, glycerolipid metabolism, and fatty acid biosynthesis during lipid synthesis. On the other hand, the expression levels of ACC, KASII, SAD, FAD2, FAD3, and PDAT genes were downregulated at 88-130 DAP compared with 60-74 DAP, which might be the key genes regulating the reduction of free fatty acid content in WOBs. In addition, 21 FAD genes were identified, including seven SAD genes, three FAD2 genes, five FAD3 genes, one FAD5 gene, one FAD6 gene, and four FAD7/8 genes. These genes were closely related to the synthesis of unsaturated fatty acids in WOBs, especially FAD2 and FAD3. The findings offered valuable insights into the dynamic changes in lipids and genetic resources and provided a foundation for walnut quality improvement.

Integrating ATAC-seq and RNA-seq to reveal the dynamics of chromatin accessibility and gene expression in regulating aril coloration of Taxus mairei

Fruit coloration results from a complex process. Maire yew (Taxus mairei) is an evergreen tree with red, purple, and yellow fruits (arils). While significant progress has been made in understanding pigment biosynthesis in arils, the role of chromatin accessibility in color development remains less well understood. To gain deeper insights into the genetic and epigenetic factors involved, we employed RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq). By integrating the results, we identified 723 differentially expressed genes (DEGs) with chromatin changes in P vs. R, including 312 up- and 411 down-regulated genes. In Y vs. R, we found 159 DEGs, with 97 up- and 62 down-regulated. KEGG enrichment analysis highlighted the flavonoid and carotenoid pathways as major contributors to color variation. When the arils turned purple, the expression levels of C4H, CHS, C3'H, F3'H, F3H, DFR, PSY, PDS, β-OHase, CYP97A3, and LUT1 were significantly up-regulated, while ZDS was down-regulated. The transition to yellow arils was characterized by the up-regulation of F3H, DFR, ZDS, CYP97A3, β-OHase, and LUT1, accompanied by the down-regulation of C4H, CHS, PSY, and PDS. Additionally, 27 transcription factors (TFs) were identified, including MYB, bHLH, and bZIP. These TFs may potentially influence variation in aril color by regulating downstream genes. In total, eight genes were selected for qRT-PCR validation, indicating the reliability of the transcriptome sequencing data. Our results provide in-depth information regarding the coloration of the arils in Maire yew. The study could provide insights for further genetic improvement in Taxus.

Correlation with Apoptosis Process through RNA-Seq Data Analysis of Hep3B Hepatocellular Carcinoma Cells Treated with Glehnia littoralis Extract (GLE)

Glehnia littoralis is a perennial herb found in coastal sand dunes throughout East Asia. This herb has been reported to have hepatoprotective, immunomodulatory, antioxidant, antibacterial, antifungal, anti-inflammatory, and anticancer activities. It may be effective against hepatocellular carcinoma (HCC). However, whether this has been proven through gene-level RNA-seq analysis is still being determined. Therefore, we are attempting to identify target genes for the cell death process by analyzing the transcriptome of Hep3B cells among HCC treated with GLE (Glehnia littoralis extract) using RNA-seq. Hep3B was used for the GLE treatment, and the MTT test was performed. Hep3B was then treated with GLE at a set concentration of 300 μg/mL and stored for 24 h, followed by RNA isolation and sequencing. We then used the data to create a plot. As a result of the MTT analysis, cell death was observed when Hep3B cells were treated with GLE, and the IC50 was about 300 μg/mL. As a result of making plots using the RNA-seq data of Hep3B treated with 300 μg/mL GLE, a tendency for the apoptotic process was found. Flow cytometry and annexin V/propidium iodide (PI) staining verified the apoptosis of HEP3B cells treated with GLE. Therefore, an increase or decrease in the DEGs involved in the apoptosis process was confirmed. The top five genes increased were GADD45B, DDIT3, GADD45G, CHAC1, and PPP1R15A. The bottom five genes decreased were SGK1, CX3CL1, ZC3H12A, IER3, and HNF1A. In summary, we investigated the RNA-seq dataset of GLE to identify potential targets that may be involved in the apoptotic process in HCC. These goals may aid in the identification and management of HCC.

Identification of MYB Transcription Factor, a Regulator Related to Hydrolysable Tannin Synthesis in Canarium album L., and Functional Analysis of CaMYBR04

Hydrolysed tannins (HTs) are polyphenols, which are related to the astringency, flavour, colour, stability, medicinal value and other characteristics of many fruits and vegetables. The biosynthetic mechanism of the majority of HTs remains unknown, and many biosynthetic pathways of HTs are speculative conclusions that have not been confirmed. The fruit of Canarium album L. (Chinese olive), which is notable for its pharmacological and edible properties, is rich in HTs. The fruit has a distinctive bitter and astringent taste when initially consumed, which mellows to a sweet sensation upon chewing. HTs serve as the primary material basis for the formation of the Chinese olive fruit's astringent quality and pharmacological effects. In this study, the fruit of C. album Changying was utilised as the research material. The objective of this study was to provide a theoretical basis for the quality control of Chinese olive fruit and the application and development of its medicinal value. In addition, the study aimed to identify and screen related MYB transcription factors involved in the synthesis of HTs in the fruit and to clarify the mechanism of MYBs in the process of synthesis and regulation of HTs in Chinese olive fruit. The principal findings were as follows. A total of 83 differentially expressed Chinese olive MYB transcription factors (CaMYBs) were identified, including 54 1R-MYBs (MYB-related), 25 2R-MYBs (R2R3-MYBs), 3 3R-MYBs, and 1 4R-MYB. Through trend analysis and correlation analysis, it was found that CaMYBR04 (Isoform0032534) exhibited a significantly higher expression (FPKM) than the other CaMYBs. The full-length cDNA sequence of CaMYBR04 was cloned and transformed into strawberry. The results demonstrated that CaMYBR04 significantly enhanced the fruit's hydrolysable tannin content. Consequently, this study elucidated the function of CaMYBR04, a regulator of the Chinese olive fruit hydrolysable tannin synthesis pathway, and established a theoretical foundation for the synthesis and regulation of fruit HTs.

Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis

Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content, which has been linked to a variety of pharmacological benefits and crucial health-promoting impacts in humans. The progress in understanding the molecular mechanisms of flavonoid accumulation in this plant has been hindered due to the deficiency of genomic and transcriptomic resources. We utilized a combination of Illumina and Oxford Nanopore Technology (ONT) sequencing to generate a de novo hybrid transcriptome assembly. In total, 126,977 unigenes were characterized, out of which 107,977 were successfully annotated in seven public databases. Within the annotated unigenes, 3,781 were categorized into 58 transcription factor families. Furthermore, we investigated the presence of four valuable flavonoids-quercetin-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, and kaempferol-3-O-β-D-glucoside in 98 samples, using high-performance liquid chromatography. A weighted gene co-expression network analysis identified two co-expression modules, MEpink and MEturquoise, that showed strong positive correlation with flavonoid content. Within these modules, four transcription factor genes (R2R3-MYB, NAC, WD40, and ARF) and four key enzyme-encoding genes (CHI, F3H, PAL, and C4H) emerged as potential hub genes. Among them, the R2R3-MYB (LcsMYB123) as a homologous gene to AtMYB123/TT2, was speculated to play a significant role in flavonol biosynthesis based on phylogenetic analysis. Our findings provided a theoretical foundation for further research into the molecular mechanisms of flavonoid biosynthesis. Additionally, The hybrid transcriptome sequences will serve as a valuable molecular resource for the transcriptional annotation of L. coreana var. sinensis, which will contribute to the improvement of high-flavonoid materials.

Integration of genome-wide association studies, metabolomics, and transcriptomics reveals phenolic acid- and flavonoid-associated genes and their regulatory elements under drought stress in rapeseed flowers

Introduction

Biochemical and metabolic processes help plants tolerate the adverse effects of drought. In plants accumulating bioactive compounds, understanding the genetic control of the biosynthesis of biochemical pathways helps the discovery of candidate gene (CG)-metabolite relationships.

Methods

The metabolic profile of flowers in 119 rapeseed (Brassica napus) accessions was assessed over two irrigation treatments, one a well-watered (WW) condition and the other a drought stress (DS) regime. We integrated information gained from 52,157 single-nucleotide polymorphism (SNP) markers, metabolites, and transcriptomes to identify linked SNPs and CGs responsible for the genetic control of flower phenolic compounds and regulatory elements.

Results

In a genome-wide association study (GWAS), of the SNPs tested, 29,310 SNPs were qualified to assess the population structure and linkage disequilibrium (LD), of which several SNPs for radical scavenging activity (RSA) and total flavanol content (TFLC) were common between the two irrigation conditions and pleiotropic SNPs were found for chlorogenic and coumaric acids content. The principal component analysis (PCA) and stepwise regression showed that chlorogenic acid and epicatechin in WW and myricetin in DS conditions were the most important components for RSA. The hierarchical cluster analysis (HCA) showed that vanillic acid, myricetin, gallic acid, and catechin were closely associated in both irrigation conditions. Analysis of GWAS showed that 60 CGs were identified, of which 18 were involved in stress-induced pathways, phenylpropanoid pathway, and flavonoid modifications. Of the CGs, PAL1, CHI, UGT89B1, FLS3, CCR1, and CYP75B137 contributed to flavonoid biosynthetic pathways. The results of RNA sequencing (RNA-seq) revealed that the transcript levels of PAL, CHI, and CYP75B137 known as early flavonoid biosynthesis-related genes and FLS3, CCR1, and UGT89B1 related to the later stages were increased during drought conditions. The transcription factors (TFs) NAC035 and ERF119 related to flavonoids and phenolic acids were upregulated under drought conditions.

Discussion

These findings expand our knowledge on the response mechanisms to DS, particularly regarding the regulation of key phenolic biosynthetic genes in rapeseed. Our data also provided specific linked SNPs for marker-assisted selection (MAS) programs and CGs as resources toward realizing metabolomics-associated breeding of rapeseed.

Integration of Metabolomics and Transcriptomics to Explore Dynamic Alterations in Fruit Color and Quality in 'Comte de Paris' Pineapples during Ripening Processes

Pineapple color yellowing and quality promotion gradually manifest as pineapple fruit ripening progresses. To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid contents as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Integration analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, RNA-seq analysis showed that structural genes, such as FLS, FNS, F3H, DFR, ANR, and GST, in the flavonoid biosynthetic pathway were upregulated, whereas the COMT, CCR, and CAD genes involved in lignin metabolism were downregulated as fruit ripening progressed. APX as well as PPO, and ACO genes related to the organic acid accumulations were upregulated and downregulated, respectively. Importantly, a comprehensive regulatory network encompassing genes that contribute to the metabolism of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlie fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.

Toward the bioactive potential of myricitrin in food production: state-of-the-art green extraction and trends in biosynthesis

Myricitrin is a member of flavonols, natural phenolic compounds extracted from plant resources. It has gained great attention for various biological activities, such as anti-inflammatory, anti-cancer, anti-diabetic, as well as cardio-/neuro-/hepatoprotective activities. These effects have been demonstrated in both in vitro and in vivo models, making myricitrin a favorable candidate for the exploitation of novel functional foods with potential protective or preventive effects against diseases. This review summarized the health benefits of myricitrin and attempted to uncover its action mechanism, expecting to provide a theoretical basis for their application. Despite enormous bioactive potential of myricitrin, low production, high cost, and environmental damage caused by extracting it from plant resources greatly constrain its practical application. Fortunately, innovative, green, and sustainable extraction techniques are emerging to extract myricitrin, which function as alternatives to conventional techniques. Additionally, biosynthesis based on synthetic biology plays an essential role in industrial-scale manufacturing, which has not been reported for myricitrin exclusively. The construction of microbial cell factories is absolutely an appealing and competitive option to produce myricitrin in large-scale manufacturing. Consequently, state-of-the-art green extraction techniques and trends in biosynthesis were reviewed and discussed to endow an innovative perspective for the large-scale production of myricitrin.

Metabolome, Plant Hormone, and Transcriptome Analyses Reveal the Mechanism of Spatial Accumulation Pattern of Anthocyanins in Peach Flesh

Anthocyanins are important secondary metabolites in fruits, and anthocyanin accumulation in the flesh of peach exhibits a spatial pattern, but the relevant mechanism is still unknown. In this study, the yellow-fleshed peach, cv. 'Jinxiu', with anthocyanin accumulation in the mesocarp around the stone was used as the experimental material. Red flesh (RF) and yellow flesh (YF) were sampled separately for flavonoid metabolite (mainly anthocyanins), plant hormone, and transcriptome analyses. The results showed that the red coloration in the mesocarp was due to the accumulation of cyanidin-3-O-glucoside, with an up-regulation of anthocyanin biosynthetic genes (F3H, F3'H, DFR, and ANS), transportation gene GST, and regulatory genes (MYB10.1 and bHLH3). Eleven ERFs, nine WRKYs, and eight NACs were also defined as the candidate regulators of anthocyanin biosynthesis in peach via RNA-seq. Auxin, cytokinin, abscisic acid (ABA), salicylic acid (SA), and 1-aminocyclopropane-1-carboxylic acid (ACC, ethylene precursor) were enriched in the peach flesh, with auxin, cytokinin, ACC, and SA being highly accumulated in the RF, but ABA was mainly distributed in the YF. The activators and repressors in the auxin and cytokinin signaling transduction pathways were mostly up-regulated and down-regulated, respectively. Our results provide new insights into the regulation of spatial accumulation pattern of anthocyanins in peach flesh.

Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses

MAIN CONCLUSION

This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.