Combined Analysis of Transcriptome and Metabolome Reveals the Potential Mechanism of Coloration and Fruit Quality in Yellow and Purple Passiflora edulis Sims

R2R3-MYB transcription factor CsMYB60 controls mature fruit skin color by regulating flavonoid accumulation in cucumber

Skin color is an important trait that determines the cosmetic appearance and quality of fruits. In cucumber, the skin color ranges from white to brown in mature fruits. However, the genetic basis for this important trait remains unclear. We conducted a genome-wide association study of natural cucumber populations, along with map-based cloning techniques, on an F2 population resulting from a cross between Pepino (with yellow-brown fruit skin) and Zaoer-N (with creamy fruit skin). We identified CsMYB60 as a candidate gene responsible for skin coloration in mature cucumber fruits. In cucumber accessions with white to pale yellow skin color, a premature stop mutation (C to T) was found in the second exon region of CsMYB60, whereas light yellow cucumber accessions exhibited splicing premature termination caused by an intronic mutator-like element insertion in CsMYB60. Transgenic CsMYB60c cucumber plants displayed a yellow-brown skin color by promoting accumulation of flavonoids, especially hyperoside, a yellow-colored flavonol. CsMYB60c encodes a nuclear protein that primarily acts as a transcriptional activator through its C-terminal activation motif. RNA sequencing and DNA affinity purification sequencing assays revealed that CsMYB60c promotes skin coloration by directly binding to the YYTACCTAMYT motif in the promoter regions of flavonoid biosynthetic genes, including CsF3'H, which encodes flavonoid 3'-hydroxylase. The findings of our study not only offer insight into the function of CsMYB60 as dominantly controlling fruit coloration, but also highlight that intronic DNA mutations can have a similar phenotypic impact as exonic mutations, which may be valuable in future cucumber breeding programs.

A 224-bp Indel in the Promoter of PeMYB114 Accounts for Anthocyanin Accumulation of Skin in Passion Fruit (Passiflora spp.)

Passion fruit (Passiflora spp.) is an important fruit tree in the family Passifloraceae. The color of the fruit skin, a significant agricultural trait, is determined by the content of anthocyanin in passion fruit. However, the regulatory mechanisms behind the accumulation of anthocyanin in different passion fruit skin colors remain unclear. In the study, we identified and characterized a R2R3-MYB transcription factor, PeMYB114, which functions as a transcriptional activator in anthocyanin biosynthesis. Yeast one-hybrid system and dual-luciferase analysis showed that PeMYB114 could directly activate the expression of anthocyanin structural genes (PeCHS and PeDFR). Furthermore, a natural variation in the promoter region of PeMYB114 alters its expression. PeMYB114purple accessions with the 224-bp insertion have a higher anthocyanin level than PeMYB114yellow accessions with the 224-bp deletion. The findings enhance our understanding of anthocyanin accumulation in fruits and provide genetic resources for genome design for improving passion fruit quality.

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae)

BACKGROUND

Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and hepatoprotective functions. However, little is known regarding the lignan biosynthesis in H. pedunculosum. In this study, we used metabolomic (non-targeted UHPLC-MS/MS) and transcriptome (RNA-Seq) analyses to identify key metabolites and genes (both structural and regulatory) associated with lignan production during the green mature (GM) and yellow mature (YM) stages of H. pedunculosum.

RESULTS

The contents of 26 lignan-related metabolites and the expression of 30 genes involved in the lignan pathway differed considerably between the GM and YM stages; most of them were more highly expressed in YM than in GM. UPLC-Q-TOF/MS confirmed that three Herpetospermum-specific lignans (including herpetrione, herpetotriol, and herpetin) were found in YM, but were not detected in GM. In addition, we proposed a lignan biosynthesis pathway for H. pedunculosum based on the fundamental principles of chemistry and biosynthesis. An integrated study of the transcriptome and metabolome identified several transcription factors, including HpGAF1, HpHSFB3, and HpWOX1, that were highly correlated with the metabolism of lignan compounds during seed ripening. Furthermore, functional validation assays revealed that the enzyme 4-Coumarate: CoA ligase (4CL) catalyzes the synthesis of hydroxycinnamate CoA esters.

CONCLUSION

These results will deepen our understanding of seed lignan biosynthesis and establish a theoretical basis for molecular breeding of H. pedunculosum.

Transcriptome, Plant Hormone, and Metabolome Analysis Reveals the Mechanism of Purple Pericarp Formation in 'Zihui' Papaya (Carica papaya L.)

The color of the pericarp is a crucial characteristic that influences the marketability of papaya fruit. Prior to ripening, normal papaya exhibits a green pericarp, whereas the cultivar 'Zihui' displays purple ring spots on the fruit tip, which significantly affects the fruit's visual appeal. To understand the mechanism behind the formation of purple pericarp, this study performed a thorough examination of the transcriptome, plant hormone, and metabolome. Based on the UPLC-ESI-MS/MS system, a total of 35 anthocyanins and 11 plant hormones were identified, with 27 anthocyanins and two plant hormones exhibiting higher levels of abundance in the purple pericarp. In the purple pericarp, 14 anthocyanin synthesis genes were up-regulated, including CHS, CHI, F3H, F3'5'H, F3'H, ANS, OMT, and CYP73A. Additionally, through co-expression network analysis, three MYBs were identified as potential key regulators of anthocyanin synthesis by controlling genes encoding anthocyanin biosynthesis. As a result, we have identified numerous key genes involved in anthocyanin synthesis and developed new insights into how the purple pericarp of papaya is formed.

Integrated Metabolomic and Transcriptomic Profiles Provide Insights into the Mechanisms of Anthocyanin and Carotenoid Biosynthesis in Petals of Medicago sativa ssp. sativa and Medicago sativa ssp. falcata

The petals of Medicago sativa ssp. sativa and M. sativa ssp. falcata are purple and yellow, respectively. Free hybridization between M. sativa ssp. sativa and M. sativa ssp. falcata has created hybrids with various flower colors in nature. Moreover, the flower colors of alfalfa are closely correlated with yield, nutritional quality, stress tolerance and other agronomic characteristics. To elucidate the underlying mechanisms of flower color formation in M. sativa ssp. sativa and M. sativa ssp. falcata, we conducted an integrative analysis of the transcriptome and metabolome of alfalfa with three different petal colors (purple, yellow and cream). The metabolic profiles suggested that anthocyanins and carotenoids are the crucial pigments in purple and yellow flowers, respectively. A quantitative exploration of the anthocyanin and carotenoid components indicated that the accumulations of cyanidin, delphinidin, peonidin, malvidin, pelargonidin and petunidin derivatives are significantly higher in purple flowers than in cream flowers. In addition, the content of carotenes (phytoene, α-carotene and β-carotene) and xanthophylls (α-cryptoxanthin, lutein, β-cryptoxanthin, zeaxanthin, antheraxanthin and violaxanthin derivatives) was markedly higher in yellow flowers than in cream flowers. Furthermore, we found that delphinidin-3,5-O-diglucoside and lutein were the predominant pigments accumulated in purple and yellow flowers, respectively. The transcriptomic results revealed that twenty-five upregulated structural genes (one C4H, three 4CL, twelve CHS, two CHI, one F3H, one F3'H, one F3'5'H and four DFR) are involved in the accumulation of anthocyanins in purple flowers, and nine structural genes (two PSY, one ZDS, two CRTISO, two BCH, one ZEP and one ECH) exert an effect on the carotenoid biosynthesis pathway in yellow flowers. The findings of this study reveal the underlying mechanisms of anthocyanin and carotenoid biosynthesis in alfalfa with three classic flower colors.

Primary Metabolite Screening Shows Significant Differences between Embryogenic and Non-Embryogenic Callus of Tamarillo (Solanum betaceum Cav.)

Tamarillo is a solanaceous tree that has been extensively studied in terms of in vitro clonal propagation, namely somatic embryogenesis. In this work, a protocol of indirect somatic embryogenesis was applied to obtain embryogenic and non-embryogenic callus from leaf segments. Nuclear magnetic resonance spectroscopy was used to analyze the primary metabolome of these distinct calli to elucidate possible differentiation mechanisms from the common genetic background callus. Standard multivariate analysis methods were then applied, and were complemented by univariate statistical methods to identify differentially expressed primary metabolites and related metabolic pathways. The results showed carbohydrate and lipid metabolism to be the most relevant in all the calli assayed, with most discriminant metabolites being fructose, glucose and to a lesser extent choline. The glycolytic rate was higher in embryogenic calli, which shows, overall, a higher rate of sugar catabolism and a different profile of phospholipids with a choline/ethanolamine analysis. In general, our results show that a distinct primary metabolome between embryogenic and non-embryogenic calli occurs and that intracellular levels of fructose and sucrose and the glucose to sucrose ratio seem to be good candidates as biochemical biomarkers of embryogenic competence.

Metabolomic and transcriptomic analyses reveal the effects of grafting on blood orange quality

Introduction

Blood orange (Citrus sinensis L.) is a valuable source of nutrition because it is enriched in anthocyanins and has high organoleptic properties. Grafting is commonly used in citriculture and has crucial effects on various phenotypes of the blood orange, including its coloration, phenology, and biotic and abiotic resistance. Still, the underlying genetics and regulatory mechanisms are largely unexplored.

Methods

In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at eight developmental stages of the lido blood orange cultivar (Citrus sinensis L. Osbeck cv. Lido) grafted onto two rootstocks.

Results and discussion

The Trifoliate orange rootstock provided the best fruit quality and flesh color for Lido blood orange. Comparative metabolomics suggested significant differences in accumulation patterns of metabolites and we identified 295 differentially accumulated metabolites. The major contributors were flavonoids, phenolic acids, lignans and coumarins, and terpenoids. Moreover, transcriptome profiling resulted in the identification of 4179 differentially expressed genes (DEGs), and 54 DEGs were associated with flavonoids and anthocyanins. Weighted gene co-expression network analysis identified major genes associated to 16 anthocyanins. Furthermore, seven transcription factors (C2H2, GANT, MYB-related, AP2/ERF, NAC, bZIP, and MYB) and five genes associated with anthocyanin synthesis pathway (CHS, F3H, UFGT, and ANS) were identified as key modulators of the anthocyanin content in lido blood orange. Overall, our results revealed the impact of rootstock on the global transcriptome and metabolome in relation to fruit quality in lido blood orange. The identified key genes and metabolites can be further utilized for the quality improvement of blood orange varieties.

Shotgun proteomics reveals changes in the pectoralis major muscle of broilers supplemented with passion fruit seed oil under cyclic heat stress conditions

The aim of this study was to characterize the proteins differentially expressed in the pectoralis major muscle of broilers supplemented with passion fruit seed oil (PFSO) under cyclic heat stress conditions. Ninety one-day-old male chicks were housed in cages arranged in a climatic chamber, where they were kept under cyclic heat stress for eight hours a day from the beginning to the end of the experiment. The birds were divided into two experimental groups, one group supplemented with 0.9% PFSO and a control group (CON) without PFSO supplementation. At 36 days of age, 18 birds were slaughtered to collect muscle samples. From pools of breast fillet samples from each group, proteolytic cleavage of the protein extracts was performed, and later, the peptides were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The 0.9% PFSO supplementation revealed the modulation of 57 proteins in the pectoralis major muscle of broilers exposed to cyclic heat stress. Among them, four proteins were upregulated, and 46 proteins were downregulated. In addition, seven proteins were expressed only in the CON group. These results suggest that PFSO may increase heat tolerance, with a possible reduction in oxidative stress, activation of neuroprotective mechanisms, protection against apoptosis, decrease in inflammatory responses, and regulation of energy metabolism.

Metabolomics and transcriptomics strategies to reveal the mechanism of diversity of maize kernel color and quality

BACKGROUND

Maize has many kernel colors, from white to dark black. However, research on the color and nutritional quality of the different varieties is limited. The color of the maize grain is an important characteristic. Colored maize is rich in nutrients, which have received attention for their role in diet-related chronic diseases and have different degrees of anti-stress protection for animal and human health.

METHODS

A comprehensive metabolome (LC-MS/MS) and transcriptome analysis was performed in this study to compare different colored maize varieties from the perspective of multiple recombination in order to study the nutritional value of maize with different colors and the molecular mechanism of color formation.

RESULTS

Maize kernels with diverse colors contain different types of health-promoting compounds, highlighting that different maize varieties can be used as functional foods according to human needs. Among them, red-purple and purple-black maize contain more flavonoids than white and yellow kernels. Purple-black kernels have a high content of amino acids and nucleotides, while red-purple kernels significantly accumulate sugar alcohols and lipids.

CONCLUSION

Our study can provide insights for improving people's diets and provide a theoretical basis for the study of food structure for chronic diseases.

Widely targeted metabolome profiling of different plateau raspberries and berry parts provides innovative insight into their antioxidant activities

Raspberries are highly nutritious and have powerful antioxidant properties, making them functional berries with positive effects on physiological functioning. However, there is limited information available on the diversity and variability of metabolites in raspberry and its parts, especially in plateau raspberries. To address this, commercial raspberries and their pulp and seeds from two plateaus in China were subjected to LC-MS/MS-based metabolomics analysis and evaluated for antioxidant activity using four assays. A metabolite-metabolite correlation network was established based on antioxidant activity and correlation analysis. The results showed that 1661 metabolites were identified and classified into 12 categories, with significant variations in composition between the whole berry and its parts from different plateaus. Flavonoids, amino acids and their derivatives, and phenolic acids were found to be up-regulated in Qinghai's raspberry compared to Yunnan's raspberry. The main differently regulated pathways were related to flavonoid, amino acid, and anthocyanin biosynthesis. The antioxidant activity of Qinghai's raspberry was stronger than Yunnan's raspberry, and the order of antioxidant capacity was seed > pulp > berry. The highest FRAP (420.31 µM TE/g DW) values was found in the seed of Qinghai's raspberry. Overall, these findings suggest that the environment in which the berries grow can affect their chemical composition, and comprehensive exploitation and cultivation of whole raspberry and its parts from different plateaus can lead to new opportunities for phytochemical compositions and antioxidant activity.

Transcriptome Analysis of Key Genes Involved in Color Variation between Blue and White Flowers of Iris bulleyana

Iris bulleyana Dykes (Southwest iris) is an extensively distributed Iridaceae species with blue or white flowers. Hereby, we performed a systematic study, employing metabolomics and transcriptomics to uncover the subtle color differentiation from blue to white in Southwest iris. Fresh flower buds from both cultivars were subjected to flavonoid/anthocyanin and carotenoid-targeted metabolomics along with transcriptomic sequencing. Among 297 flavonoids, 24 anthocyanins were identified, and 13 showed a strong down-accumulation pattern in the white flowers compared to the blue flowers. Significant downregulation of 3GT and 5GT genes involved in the glycosylation of anthocyanins was predicted to hinder the accumulation of anthocyanins, resulting in white coloration. Besides, no significant altered accumulation of carotenoids and expression of their biosynthetic genes was observed between the two cultivars. Our study systematically addressed the color differentiation in I. bulleyana flowers, which can aid future breeding programs.

Transcriptomic and metabolomic profiling of flavonoid biosynthesis provides novel insights into petals coloration in Asian cotton (Gossypium arboreum L.)

BACKGROUND

Asian cotton (Gossypium arboreum L.), as a precious germplasm resource of cotton with insect resistance and stress tolerance, possesses a broad spectrum of phenotypic variation related to pigmentation. Flower color affects insect pollination and the ornamental value of plants. Studying flower color of Asian cotton varieties improves the rate of hybridization and thus enriches the diversity of germplasm resources. Meanwhile, it also impacts the development of the horticultural industry. Unfortunately, there is a clear lack of studies concerning intricate mechanisms of cotton flower-color differentiation. Hereby, we report an integrative approach utilizing transcriptome and metabolome concerning flower color variation in three Gossypium arboreum cultivars.

RESULTS

A total of 215 differentially accumulated metabolites (DAMs) were identified, including 83 differentially accumulated flavonoids (DAFs). Colorless kaempferol was more abundant in white flowers, while gossypetin-fer showed specificity in white flowers. Quercetin and gossypetin were the main contributors to yellow petal formation. Pelargonidin 3-O-beta-D-glucoside and cyanidin-3-O-(6''-Malonylglucoside) showed high accumulation levels in purple petals. Quercetin and gossypetin pigments also promoted purple flower coloration. Moreover, 8178 differentially expressed genes (DEGs) were identified by RNA sequencing. The correlation results between total anthocyanins and DEGs were explored, indicating that 10 key structural genes and 29 transcription factors promoted anthocyanin biosynthesis and could be candidates for anthocyanin accumulation. Ultimately, we constructed co-expression networks of key DAFs and DEGs and demonstrated the interactions between specific metabolites and transcripts in different color flowers.

CONCLUSION

This study provides new insights into elucidating the regulatory mechanisms of cotton flower color and lays a potential foundation for generate cotton varieties with highly attractive flowers for pollinators.

Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Flavonoid Accumulation and Its Underlying Mechanism in Fruits of Distinct Canarium album Cultivars

Canarium album fruit has great potential to be consumed as a raw material not only for food but also medicine. The diverse active metabolites composition and content of C. album fruits greatly affect their pharmacological effects. However, up to now, there has been no report on the global metabolome differences among fruits from distinct C. album cultivars. In our present study, by using non-targeted metabolomics techniques, we identified 87 DAMs (differentially accumulated metabolites) including 17 types of flavonoids from fruits of four different C. album cultivars. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that the flavone and flavonol biosynthesis- and flavonoid biosynthesis-related DAMs were major factors determining their metabolome differences. Comparative transcriptomic analysis revealed that 15 KEGG pathways were significantly enriched by genes of the identified 3655 DEGs (differentially expressed genes) among different C. album cultivars. Consistent with the metabolome data, flavonoid biosynthesis-related DEGs, including eight key structural genes (such as FLS, CCoAOMT, CHI, C4H, DFR, LAR, and C3′H, etc.) and several regulatory transcription factor (TF) genes (including 32 MYBs and 34 bHLHs, etc.), were found to be significantly enriched (p < 0.01). Our study indicated that the differential expression of flavonoid biosynthesis-related genes and accumulation of flavonoids played dominant roles in the various metabolome compositions of fruits from different C. album cultivars.

Insight into the molecular mechanisms of leaf coloration in Cymbidium ensifolium

Cymbidiumensifolium L. is a significant ornamental plant in Orchidaceae. Aside from its attractive flowers, its leaf coloration is also an important ornamental trait. However, there is an apparent lack of studies concerning the intricate mechanism of leaf coloration in C. ensifolium. In this study, we report a systematic evaluation of leaf coloration utilizing transcriptome and metabolome profiles of purple, yellow, and green leaves. In total, 40 anthocyanins and 67 flavonoids were quantified along with chlorophyll content. The tissue–transcriptome profile identified 26,499 differentially expressed genes (DEGs). The highest chlorophyll contents were identified in green leaves, followed by yellow and purple leaves. We identified key anthocyanins and flavonoids associated with leaf coloration, including cyanidin-3-O-sophoroside, naringenin-7-O-glucoside, delphinidin, cyanidin, petunidin, and quercetin, diosmetin, sinensetin, and naringenin chalcone. Moreover, genes encoding UDP-glucoronosyl, UDP-glucosyl transferase, chalcone synthesis, flavodoxin, cytochrome P450, and AMP-binding enzyme were identified as key structural genes affecting leaf coloration in C. ensifolium. In summary, copigmentation resulting from several key metabolites modulated by structural genes was identified as governing leaf coloration in C. ensifolium. Further functional verification of the identified DEGs and co-accumulation of metabolites can provide a tool to modify leaf color and improve the aesthetic value of C. ensifolium.

Integrated Transcriptome and Metabolome Analyses Reveal the Anthocyanin Biosynthesis Pathway in AmRosea1 Overexpression 84K Poplar

Populus alba × Populus glandulosa (84K poplar) is model material with excellent genetic engineering resource and ornamental value. In our study, AmRosea1 (Antirrhinum majus) was overexpressed in 84K poplar, and the transgenic 84K (AM) poplar with high content of anthocyanin exhibited red pigmentation leaves. The transcriptome analysis between wild type (WT) and AM showed that 170 differentially expressed genes (DEGs) (86 up-regulated and 84 down-regulated) were found, and some DEGs were involved in flavone and flavonol biosynthesis, flavonoid biosynthesis and anthocyanin biosynthesis. The metabolome analysis showed that 13 anthocyanins-related differentially accumulated metabolites (DAMs) were detected in AM. The correlation analysis between DEGs and DAMs were performed, and the results revealed that 18 DEGs, including 11 MYB genes, two BZ1 genes, one FG2 gene, one ANS gene, and three IF7MAT genes, were negatively or positively correlated with 13 DAMs. The phylogenetic analysis demonstrated that there was high homology between AmRosea1 and PagMYB113, and MYB113 co-expressed with BZ1, ANS and DFR directly. Our results elucidated the molecular mechanism of plant color change mediated by anthocyanin biosynthesis pathway, which laid the foundation for the development and utilization of colorful woody plant.

Phytochemical Compositions and Antioxidant Activities of Essential Oils Extracted from the Flowers of Paeonia delavayi Using Supercritical Carbon Dioxide Fluid

Essential oils were extracted from dark-purple, red and yellow petals of Paeonia delavayi using Supercritical Carbon Dioxide method. The compositions of essential oils were analyzed using gas chromatography-mass spectrometry (GC-MS). Antioxidant activity assays were carried out using DPPH, ABTS- and FRAP methods. Total polyphenols and total flavonoids were measured to evaluate the in vitro antioxidant activity in addition to the volatile compounds contained in the essential oils extracted from the flower petals of P. delavayi with the three flower colors. A total of 194 compounds were detected from essential oils of P. delavayi flowers, including 83 in dark-purple petals, 90 in red petals and 80 in yellow petals. These compounds mainly include alcohols, aldehydes, ketones, alkenes, alkanes, esters and polyphenols. The results showed that the volatile compounds accumulated differentially among the essential oils from the different colors of flower petals. Principal component analysis (PCA) indicated that essential oils derived from dark-purple and red petals were more closely clustered while the yellow petal essential oil was very different with both the purple-red and red. Antioxidant assays suggested that the radical scavenging activity and the iron reduction antioxidant activity in the essential oils were highly correlated with the flower petal colors. These results suggest P. delavayi flower petals are potentially good resources for high quality essential oils and natural antioxidants.

Combining Metabolomics and Transcriptomics to Reveal the Mechanism of Coloration in Purple and Cream Mutant of Sweet Potato (Ipomoea batatas L.)

Purple sweet potato is considered as a healthy food because of its high anthocyanins. To understand the coloring mechanism and quality change between purple-fleshed sweet potato (cv. Xuzi201) and its cream fleshed mutant (M1001), a combined metabolomic and transcriptomic analysis was performed. The metabolome data showed that 4 anthocyanins, 19 flavones, 6 flavanones, and 4 flavonols dramatically decreased in M1001, while the contents of 3 isoflavones, 3 flavonols, 4 catechins, and 2 proanthocyanins increased. Transcriptomic analyses indicated that the expression of 49 structural genes in the flavonoid pathway and transcription factors (TFs) (e.g., bHLH2, R2R3-MYB, MYB1) inducting anthocyanin biosynthesis were downregulated, but the repressor MYB44 was upregulated. The IbMYB1-2 gene was detected as a mutation gene in M1001, which is responsible for anthocyanin accumulation in the storage roots. Thus, the deficiency of purple color in the mutant is due to the lack of anthocyanin accumulation which was regulated by IbMYB1. Moreover, the accumulation of starch and aromatic volatiles was significantly different between Xuzi201 and M1001. These results not only revealed the mechanism of color mutation but also uncovered certain health-promoting compounds in sweet potato.

Integrative analysis of transcriptomic and metabolomic profiles reveals new insights into the molecular foundation of fruit quality formation in Citrullus lanatus (Thunb.) Matsum. & Nakai

In this study, an integrated transcriptome and metabolome analysis was used to explore the molecular foundation of fruit quality in two parent lines of Citrullus lanatus with distinct flesh characteristics, including ‘14-1’ (sweet, red, and soft) and ‘W600’ (bitter, light yellow, and firm), as well as the corresponding F1 population (bitter, light yellow, and firm). Numerous differentially expressed genes (DEGs) were identified in the fruit samples: 3,766 DEGs for ‘14-1’ vs. ‘W600’, 2,767 for ‘14-1’ vs. F1, and 1,178 for F1 vs. ‘W600’ at the transition stage; and 4,221 for ‘14-1’ vs. ‘W600’, 2,447 for ‘14-1’ vs. F1, and 446 for F1 vs. ‘W600’ at the maturity stage. Weighted gene co-expression network analysis (WGCNA) revealed that a gene module including 1,111 DEGs was closely associated with flesh taste and color, and another gene module including 1,575 DEGs contributed significantly to flesh texture. The metabolomic results showed that there were 447 differential metabolites (DMs) for ‘14-1’ vs. ‘W600’ fruits, 394 for ‘14-1’ vs. F1, and 298 for F1 vs. ‘W600’ at the maturity stage. Combining WGNCA and metabolomic results, several DEGs and DMs were further identified as hub players in fruit quality formation: six DEGs with four DMs for flesh sweetness; six DEGs with 13 DMs for bitterness; nine DEGs with 10 DMs for flesh color; and nine DEGs with four DMs for flesh texture. Altogether, these observations not only expand our knowledge of the molecular basis of fruit quality in watermelon, but also provide potential targets for future watermelon improvement.

Comparison of Metabolome and Transcriptome of Flavonoid Biosynthesis in Two Colors of Coreopsis tinctoria Nutt

Coreopsis tinctoria Nutt. (C. tinctoria) has a long history of application and high economic and medicinal value. Flavonoids, the main active components of C. tinctoria, are widely studied in pharmacology and food development. However, the flavonoid biosynthesis pathway in C. tinctoria is unclear. In this study, we comprehensively compared the transcriptomes and metabolite profiles of two colors of C. tinctoria flowers (LS and JS) at different flowering stages. A total of 165 flavonoids (46 flavonoids, 42 flavonols, 22 anthocyanins, 18 chalcones, 12 dihydroflavonols, nine isoflavones, eight dihydroflavonoids, six flavanols, and two tannins) were identified in LS and JS at different flowering stages. Thirty-three metabolites (11 anthocyanins, 11 flavonols, seven flavonoids, two dihydroflavonols, one dihydroflavone, and one chalcone) were found to be statistically significantly different in the LS vs. JS groups. LS flowers accumulated higher levels of 10 anthocyanins (seven cyanidins and three pelargonidins) than JS flowers. Furthermore, candidate genes related to the regulation of flavonoid and anthocyanin synthesis were identified and included 28 structural genes (especially F3H, Cluster-28756.299649, and 3GT, Cluster-28756.230942) in LS and JS, six key differentially expressed transcription factors (especially MYB90a, Cluster-28756.143139) in LS and JS, and 17 other regulators (mainly including transporter proteins and others) in LS. Our results provide valuable information for further studies on the mechanism underlying flavonoid biosynthesis in C. tinctoria.

Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change

Acer pseudosieboldianum (Pax) Komarov is an ornamental plant with prominent potential and is naturally distributed in Northeast China. Here, we obtained a chromosome-scale genome assembly of A. pseudosieboldianum combining HiFi and Hi-C data, and the final assembled genome size was 690.24 Mb and consisted of 287 contigs, with a contig N50 value of 5.7 Mb and a BUSCO complete gene percentage of 98.4%. Genome evolution analysis showed that an ancient duplication occurred in A. pseudosieboldianum. Phylogenetic analyses revealed that Aceraceae family could be incorporated into Sapindaceae, consistent with the present Angiosperm Phylogeny Group system. We further construct a gene-to-metabolite correlation network and identified key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change. Additionally, we identified crucial teosinte branched1, cycloidea, and proliferating cell factors (TCP) transcription factors that might be involved in leaf morphology regulation of A. pseudosieboldianum, Acer yangbiense and Acer truncatum. Overall, this reference genome is a valuable resource for evolutionary history studies of A. pseudosieboldianum and lays a fundamental foundation for its molecular breeding.

Integrative Analysis of Metabolome and Transcriptome Reveals the Mechanism of Color Formation in Liriope spicata Fruit

Liriope spicata is an important ornamental ground cover plant, with a fruit color that turns from green to black during the development and ripening stages. However, the material basis and regulatory mechanism of the color variation remains unclear. In this study, a total of 31 anthocyanins and 2 flavonols were identified from the skin of L. spicata fruit via integrative analysis on the metabolome and transcriptome of three developmental stages. The pigments of black/mature fruits are composed of five common anthocyanin compounds, of which Peonidin 3–O–rutinoside and Delphinidin 3–O–glucoside are the most differential metabolites for color conversion. Using dual-omics joint analysis, the mechanism of color formation was obtained as follows. The expression of structural genes including 4CL, F3H, F3′H, F3′5′H and UFGT were activated due to the upregulation of transcription factor genes MYB and bHLH. As a result, a large amount of precursor substances for the synthesis of flavonoids accumulated. After glycosylation, stable pigments were generated which promoted the accumulation of anthocyanins and the formation of black skin.

Constituent Characteristics and Functional Properties of Passion Fruit Seed Extract

The genus Passiflora L. is widely cultivated in tropical and subtropical regions. The major species, Passiflora edulis Sims, is known as 'passion fruit' and is widely used in processed foods as well as eaten raw. P. edulis fruits are eaten for their pulp together with the seeds; however, the seeds are often discarded when used in processed foods. P. edulis seeds contain a variety of nutrients and functional components, and their industrial use is desirable from the perspective of waste reduction. Previous studies have analyzed the constituents of P. edulis and their physiological functions. P. edulis seeds contain various types of polyphenols, especially those rich in stilbenes (e.g., piceatannol). P. edulis seed extracts and isolated compounds from seeds have been reported to exhibit various physiological functions, such as antioxidant effects, improvement of skin condition, fat-burning promotion effects, and hypoglycemic effects. This review summarizes the nutritional characteristics, polyphenol content, and physiological functions of P. edulis seeds.

Combined transcriptome and metabolome integrated analysis of Acer mandshuricum to reveal candidate genes involved in anthocyanin accumulation

The red color formation of Acer mandshuricum leaves is caused by the accumulation of anthocyanins primarily, but the molecular mechanism researches which underlie anthocyanin biosynthesis in A. mandshuricum were still lacking. Therefore, we combined the transcriptome and metabolome and analyzed the regulatory mechanism and accumulation pattern of anthocyanins in three different leaf color states. In our results, 26 anthocyanins were identified. Notably, the metabolite cyanidin 3-O-glucoside was found that significantly correlated with the color formation, was the predominant metabolite in anthocyanin biosynthesis of A. mandshuricum. By the way, two key structural genes ANS (Cluster-20561.86285) and BZ1 (Cluster-20561.99238) in anthocyanidin biosynthesis pathway were significantly up-regulated in RL, suggesting that they might enhance accumulation of cyanidin 3-O-glucoside which is their downstream metabolite, and contributed the red formation of A. mandshuricum leaves. Additionally, most TFs (e.g., MYBs, bZIPs and bHLHs) were detected differentially expressed in three leaf color stages that could participate in anthocyanin accumulation. This study sheds light on the anthocyanin molecular regulation of anthocyanidin biosynthesis and accumulation underlying the different leaf color change periods in A. mandshuricum, and it could provide basic theory and new insight for the leaf color related genetic improvement of A. mandshuricum.

Establishment of a Novel and Efficient Agrobacterium-Mediated in Planta Transformation System for Passion Fruit (Passiflora edulis)

Passion fruit (Passiflora edulis) is an important fruit crop with high economic value. Genetic engineering plays an important role in crop improvement with desired traits and gene functional studies. The lack of a simple, efficient, and stable transformation system for passion fruit has greatly limited gene functional studies. In this study, a simple and efficient Agrobacterium-mediated in planta transformation system for passion fruit was established, using Agrobacterium virulent strain EHA105 harboring the binary vectors pCAMBIA1301 and pCAMBIA1302 with GUS and GFP reporter genes. The system requires less time and labor costs than conventional transformation systems, and no additional phytohormones and sterile conditions are required. Regeneration efficiency of 86% and transformation efficiency of 29% were achieved, when the wounds were wrapped with Parafilm and the plants were kept in darkness for 15 days. Approximately 75% of the regenerated plants had a single shoot and 26% multiple shoots. The transformation was confirmed at the DNA and RNA levels as well as by GUS staining and GFP fluorescent measurements. The developed protocol will contribute to the genetic improvement of passion fruit breeding.

Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Leaf Color Change in Chokecherry (Padus virginiana)

Chokecherry (Padus virginiana L.) is an important landscaping tree with high ornamental value because of its colorful purplish-red leaves (PRL). The quantifications of anthocyanins and the mechanisms of leaf color change in this species remain unknown. The potential biosynthetic and regulatory mechanisms and the accumulation patterns of anthocyanins in P. virginiana that determine three leaf colors were investigated by combined analysis of the transcriptome and the metabolome. The difference of chlorophyll, carotenoid and anthocyanin content correlated with the formation of P. virginiana leaf color. Using enrichment and correlation network analysis, we found that anthocyanin accumulation differed in different colored leaves and that the accumulation of malvidin 3-O-glucoside (violet) and pelargonidin 3-O-glucoside (orange-red) significantly correlated with the leaf color change from green to purple-red. The flavonoid biosynthesis genes (PAL, CHS and CHI) and their transcriptional regulators (MYB, HD-Zip and bHLH) exhibited specific increased expression during the purple-red periods. Two genes encoding enzymes in the anthocyanin biosynthetic pathway, UDP glucose-flavonoid 3-O-glucosyl-transferase (UFGT) and anthocyanidin 3-O-glucosyltransferase (BZ1), seem to be critical for suppressing the formation of the aforesaid anthocyanins. In PRL, the expression of the genes encoding for UGFT and BZ1 enzymes was substantially higher than in leaves of other colors and may be related with the purple-red color change. These results may facilitate genetic modification or selection for further improvement in ornamental qualities of P. virginiana.

Analysis of Flavonoid Metabolites in Watercress (Nasturtium officinale R. Br.) and the Non-Heading Chinese Cabbage (Brassica rapa ssp. chinensis cv. Aijiaohuang) Using UHPLC-ESI-MS/MS

Flavonoids from plants play an important role in our diet. Watercress is a special plant that is rich in flavonoids. In this study, four important watercress varieties were compared with non-heading Chinese cabbage by ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS). A total of 132 flavonoid metabolites (including 8 anthocyanins, 2 dihydroflavone, 3 dihydroflavonol, 1 flavanols, 22 flavones, 11 flavonoid carbonosides, 82 flavonols, and 3 isoflavones) were detected. Flavonoid metabolites varied widely in different samples. Both the non-heading Chinese cabbage and the variety of watercress from Guangdong, China, had their own unique metabolites. This work is helpful to better understand flavonoid metabolites between the non-heading Chinese cabbage and the other four watercress varieties, and to provide a reliable reference value for further research.

Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement

Common wheat (Triticum aestivum L.) is a leading cereal crop, but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize. The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets. Meanwhile, the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals. One such productive avenue is combining metabolomics approaches with genetic designs. However, this trial is not as widespread as that for sequencing technologies, especially when the acquisition, understanding, and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized. In this review, we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes. Considerable progress has been made in delivering improved varieties, suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and, as such, this procedure could serve as an -omics-informed roadmap for executing similar improvement strategies in wheat and other species.

Integrated transcriptome and metabolome analyses of biochar-induced pathways in response to Fusarium wilt infestation in pepper

The present study used soils contaminated with Fusarium oxysporum f. sp. capsici (CCS) and CCS amended with bamboo biochar (CCS + BC) to grow the pepper variety Qujiao No.1. The physiological performance, and transcriptome and metabolome profiling in leaf (L) and fruit (F) of Qujiao No.1 were conducted. Application of biochar improved soil properties, pepper plant nutrition and increased activities of enzymes related to pest/disease resistance, leading to superior physiological performance and lesser F. wilt disease incidence than plants from CCS. Most of the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were involved in protein processing in endoplasmic reticulum (fruit), plant pathogen interaction (fruit), photosynthesis (leaf), phenylpropanoid biosynthesis (both tissues) and metabolic pathways (both tissues). Biochar improved plant photosynthesis, enhanced the immune system, energy production and increased stress signaling pathways. Overall, our results provide evidence of a number of pathways induced by biochar in pepper regulating its response to F. wilt disease.

Impact of Various Microbial-Fermented Methods on the Chemical Profile of Dark Tea Using a Single Raw Tea Material

In the present study, we produced Pu-erh, Liubao, Qingzhuan, and Fuzhuan teas using a single raw tea material and applied widely targeted metabolomics to study the impact of various microbial-fermented methods on the chemical profile of dark tea. The contents of catechins and free amino acids decreased drastically, whereas the contents of gallic acid and theabrownins increased significantly during microbial fermentation. Pu-erh tea had the highest content of theabrownins (11.82 ± 0.49%). Moreover, MS-based metabolomics analysis revealed that the different types of dark teas were significantly different from their raw material. A total of 85 differential metabolites were screened among 569 metabolites identified referring to self-compiled database. Glycosylated, hydroxylated, methylated, and condensed and oxidated products originating from microbial bioconversion of their corresponding primitive forms were significantly increased in dark teas. These results suggest that various microbial-fermented methods greatly affect the metabolic profile of dark tea, which can provide useful information for dark tea biochemistry research.