RefMetaPlant: a reference metabolome database for plants across five major phyla.

Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC-MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A 'Reference Metabolome Database for Plants' (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like 'LC-MS/MS Query', 'RefMetaBlast' and 'CompoundLibBlast' for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.

CropMetabolome: a comprehensive metabolome database for major crops cross eight categories.

Chemical compositions of crops are of great agronomical importance, as crops serve as resources for nutrition, energy, and medicines for human and livestock. For crop metabolomics research, the lack of crop reference metabolome and high-quality reference compound mass spectra, as well as utilities for metabolic profiling, has hindered the discovery and functional study of phytochemicals in crops. To meet these challenging needs, we have developed the Crop Metabolome database (abbreviated as CropMetabolome) that is dedicated to the construction of crop reference metabolome, repository, and dissemination of crop metabolomic data, and profiling and analytic tools for metabolomics research. CropMetabolome contains a metabolomics database for more than 50 crops (belonging to eight categories) that integrated self-generated raw mass spectral data and public-source datasets. The reference metabolome for 59 crop species was constructed, which have functions that parallel those of reference genome in genomic studies. CropMetabolome also contains 'Standard compound mass spectral library', 'Flavonoids library', 'Pesticide library', and a set of related analytical tools that enable metabolic profiling based on a reference metabolome (CropRefMetaBlast), annotation and identification of new metabolites (CompoundLibBlast), deducing the structure of novel flavonoid derivatives (FlavoDiscover), and detecting possible residual pesticides in crop samples (PesticiDiscover). In addition, CropMetabolome is a repository to share and disseminate metabolomics data and a platform to promote collaborations to develop reference metabolome for more crop species. CropMetabolome is a comprehensive platform that offers important functions in crop metabolomics research and contributes to improve crop breeding, nutrition, and safety. CropMetabolome is freely available at https://www.cropmetabolome.com/.

EGR1 and EGR2 positively regulate plant ABA signaling by modulating the phosphorylation of SnRK2.2.

During abscisic acid (ABA) signaling, reversible phosphorylation controls the activity and accumulation of class III SNF1-RELATED PROTEIN KINASE 2s (SnRK2s). While protein phosphatases that negatively regulate SnRK2s have been identified, those that positively regulate ABA signaling through SnRK2s are less understood. In this study, Arabidopsis thaliana mutants of Clade E Growth-Regulating 1 and 2 (EGR1/2), which belong to the protein phosphatase 2C family, exhibited reduced ABA sensitivity in terms of seed germination, cotyledon greening, and ABI5 accumulation. Conversely, overexpression increased these ABA-induced responses. Transcriptomic data revealed that most ABA-regulated genes in egr1 egr2 plants were expressed at reduced levels compared with those in Col-0 after ABA treatment. Abscisic acid up-regulated EGR1/2, which interact directly with SnRK2.2 through its C-terminal domain I. Genetic analysis demonstrated that EGR1/2 function through SnRK2.2 during ABA response. Furthermore, SnRK2.2 de-phosphorylation by EGR1/2 was identified at serine 31 within the ATP-binding pocket. A phospho-mimic mutation confirmed that phosphorylation at serine 31 inhibited SnRK2.2 activity and reduced ABA responsiveness in plants. Our findings highlight the positive role of EGR1/2 in regulating ABA signaling, they reveal a new mechanism for modulating SnRK2.2 activity, and provide novel insight into how plants fine-tune their responses to ABA.

Three-electrode germanium-on-silicon avalanche photodiode array.

In this Letter, we report a bridge-connected three-electrode germanium-on-silicon (Ge-on-Si) avalanche photodiode (APD) array compatible with the complementary metal-oxide semiconductor (CMOS) process. In addition to the two electrodes on the Si substrate, a third electrode is designed for Ge. A single three-electrode APD was tested and analyzed. By applying a positive voltage on the Ge electrode, the dark current of the device can be reduced, and yet the response of the device can be increased. Under a dark current of 100 nA, as the voltage on Ge increases from 0 V to 15 V, the light responsivity is increased from 0.6 A/W to 1.17 A/W. We report, for the first time to the best of our knowledge, the near-infrared imaging properties of an array of three-electrode Ge-on-Si APDs. Experiments show that the device can be used for LiDAR imaging and low-light detection.

Silver-Mediated Cascade Synthesis of Functionalized 1,4-Dihydro-2H-benzo-1,3-oxazin-2-ones from Carbon Dioxide.

A conceptually novel catalytic domino approach is presented for the synthesis of highly functional 1,4-dihydro-2H-1,3-benzoxazine-2-one derivatives. Key to the chemoselectivity is a proper design of the precursor to override thermodynamically favored parasitic cyclization processes and empower the formation of the desired product through Thorpe-Ingold effects. The synthetic diversity of these CO2 -based heterocycles is further demonstrated, and the isolation of a reaction intermediate supports an unusual ring-expansion sequence from an α-alkylidene, five-membered cyclic carbonate to a six-membered cyclic carbamate by N-induced isomerization.

Two-dimensional multi-layered SiN-on-SOI optical phased array with wide-scanning and long-distance ranging.

Silicon based optoelectronic integrated optical phased array is attractive owing to large-dense integration, large scanning range and CMOS compatibility. In this paper, we design and fabricate a SiN-on-SOI two-dimensional optical phased array chip. We demonstrate a two-dimensional scanning range of 96°×14.4° and 690 mW peak power of the main lobe. Additionally, we set up the time of flight (ToF) and frequency-modulated continuous-wave (FMCW) ranging systems by using this optical phased array chip, and achieve the objects detection at the range of 20 m in the ToF system and 109 m in the FMCW system, respectively.

Co-fermented cow milk protein by Lactobacillus helveticus KLDS 1.8701 and Lactobacillus plantarum KLDS 1.0386 attenuates its allergic immune response in Balb/c mice.

Milk protein is one of the major food allergens. As an effective processing method, fermentation may reduce the potential allergenicity of allergens. This study aimed to evaluate the therapeutic potential of co-fermented milk protein using Lactobacillus helveticus KLDS 1.8701 and Lactobacillus plantarum KLDS 1.0386 in cow milk protein allergy (CMPA) management. This study determined the secondary and tertiary structures of the fermented versus unfermented proteins by Fourier-transform infrared spectroscopy and surface hydrophobicity to evaluate its conformational changes. Our results showed that different fermentation methods have significantly altered the conformational structures of the cow milk protein, especially the tertiary structure. Further, the potential allergenicity of the fermented cow milk protein was assessed in Balb/c mice, and mice treated with the unfermented milk and phosphate-buffered saline were used as a control. We observed a significant reduction in allergenicity via the results of the spleen index, serum total IgE, specific IgE, histamine, and mouse mast cell protease 1 in the mice treated with the co-fermented milk protein. In addition, we analyzed the cytokines and transcription factors expression levels of spleen and jejunum and confirmed that co-fermentation could effectively reduce the sensitization of cow milk protein by regulating the imbalance of T helper (Th1/Th2 and Treg/Th17). This study suggested that changes of conformational structure could reduce the potential sensitization of cow milk protein; thus, fermentation may be a promising strategy for developing a method of hypoallergenic dairy products.

Analysis of the complete genome sequence of Lactobacillus delbrueckii ssp. bulgaricus with post-acidification capacity and its influence on yogurt in storage.

In recent years, yogurt has been one of the most popular fermented dairy products and is sold worldwide. In this study, pH and titrated acid changes of 4 strains of Lactobacillus delbrueckii ssp. bulgaricus fermented milk during storage were detected. The difference between L. bulgaricus KLDS1.1011 and KLDS1.0207 was significant, with the latter exhibiting reduced acidity levels. Therefore, we determined the complete genome sequence of the 2 strains. Then the expression of specific genes and common genes related to glucose metabolism and proteolysis of L. bulgaricus KLDS1.1011 and KLDS1.0207 were detected by quantitative real-time reverse-transcription PCR. Analysis indicated that the key enzymes in glycometabolism and proteolysis of L. bulgaricus KLDS1.1011 were significantly different than those of L. bulgaricus KLDS1.0207. The contents of lactose and glucose decreased during storage of L. bulgaricus fermented milk, as determined by HPLC, and the contents of lactic acid and galactose increased, with L. bulgaricus KLDS1.1011 increasing less. With skim milk as a raw material, L. bulgaricus KLDS1.1011, KLDS1.0207, and Streptococcus thermophilus S1 were used as fermentation strains to yield yogurt at 42°C, and sensory evaluation was compared with yogurt fermented by commercial starter cultures. Yogurt from L. bulgaricus KLDS1.1011 was the highest-rated. Therefore, the study may provide guidelines for the development of yogurt starters.

Chemical constituents, biological activities and anti-rheumatoid arthritic properties of four citrus essential oils.

Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease with predominant synovitis that has no complete cure or preventive treatment. Citrus essential oils, used in natural fragrances, contain a variety of functional ingredients that are worthy of investigation for their potential as natural anti-inflammatory drug sources. In this study, essential oils were hydro distilled from the peels of four citrus species: Citrus sinensis (L.) Osbeck (CSEOs), Citrus paradisi Macfad. (CPEOs), Citrus limon (L.) Osbeck (CLEOs) and Citri Reticulatae Pericarpium (CREOs). Altogether, 81 compounds were identified using gas chromatography-mass spectrometry (GC-MS), of which d-limonene (17.96%-94.66%) was an abundant component of all four oils. The stable 1,1-diphenyl-2-pyrrole hydrazine (DPPH) free radical test showed that all four essential oils had excellent antioxidant properties (IC50 , 0.76-13.86 µg/mL). Furthermore, the oils remarkably increased the first G1 phase of the cell cycle, which inhibited the pro-inflammatory factor expression. An immunohistochemical analysis indicated that the four essential oils inhibited the expression of tumor necrosis factor-α and cyclooxygenase-2 and they exhibited anti-inflammatory activity in a rat model that was similar to that of the common drug, Ibuprofen. These results show that the CSEOs, CPEOs, CLEOs, and CREOs have significant antirheumatic activities and thus have great potential in developing functional food or drugs for treating RA.

Surface illuminated interdigitated Ge-on-Si photodetector with high responsivity.

To address the problem of traditional surface illuminated detectors being of low responsivity, this work proposes a large-size interdigitated "finger-type" germanium-on-silicon (Ge-on-Si) photodetector (PD) based on the surface illumination approach. For 1550 nm light with a surface incident power of -20 dBm at room temperature, the best responsivity of the PD achieved is ∼0.64 A/W at 0.5 V. At the same time, the optimal bandwidth reaches 1.537 MHz with 3.5 V applied voltage. In order to suppress the dark current induced noise, a Ge-on-Si avalanche photodiode (APD) with the interdigitated structure is designed. The avalanche voltage is designed ∼13.3 V at room temperature, and the dark current density in linear region is at mA/cm2 order. We believe this type of device can be applied in weak light detection condition.

Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients.

BACKGROUND: Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people's health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is very limited. RESULTS: An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling of Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao tissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. CONCLUSIONS: The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.

Metabolomic Analysis Reveals Domestication-Driven Reshaping of Polyphenolic Antioxidants in Soybean Seeds.

Crop domestication has resulted in nutrient losses, so evaluating the reshaping of phytonutrients is crucial for improving nutrition. Soybean is an ideal model due to its abundant phytonutrients and wild relatives. In order to unravel the domestication consequence of phytonutrients, comparative and association analyses of metabolomes and antioxidant activities were performed on seeds of six wild (Glycine soja (Sieb. and Zucc.)) and six cultivated soybeans (Glycine max (L.) Merr.). Through ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), we observed a greater metabolic diversity in wild soybeans, which also displayed higher antioxidant activities. (-)-Epicatechin, a potent antioxidant, displayed a 1750-fold greater abundance in wild soybeans than in cultivated soybeans. Multiple polyphenols in the catechin biosynthesis pathway were significantly higher in wild soybeans, including phlorizin, taxifolin, quercetin 3-O-galactoside, cyanidin 3-O-glucoside, (+)-catechin, (-)-epiafzelechin, catechin-glucoside, and three proanthocyanidins. They showed significant positive correlations with each other and antioxidant activities, indicating their cooperative contribution to the high antioxidant activities of wild soybeans. Additionally, natural acylation related to functional properties was characterized in a diverse range of polyphenols. Our study reveals the comprehensive reprogramming of polyphenolic antioxidants during domestication, providing valuable insights for metabolism-assisted fortification of crop nutrition.

Physiological and transcriptomic evidence of antioxidative system and ion transport in chromium detoxification in germinating seedlings of soybean.

Chromium (Cr) toxicity impairs the productivity of crops and is a major threat to food security worldwide. However, the effect of Cr toxicity on seed germination and transcriptome of germinating seedlings of soybean crop has not been fully explored. In this study, two Cr-tolerant lines (J82, S125) and two Cr-sensitive ones (LD1, RL) were screened out of twenty-one soybean (Glycine max L.) genotypes based on seed germination rate, seed germinative energy, seed germination index, and growth of germinating seedlings under 50 mg L-1 Cr treatment. We found that Cr stress inhibits the growth of soybean seed germinating seedlings due to the Cr-induced overaccumulation of reactive oxygen species (ROS). Significantly different levels of element contents, antioxidant enzyme activities, malondialdehyde content were observed in the four soybean genotypes with contrasting Cr tolerance. Further, a total of 13,777 differentially expressed genes (DEGs) were identified in transcriptomic sequencing and 1298 DEGs in six gene modules were found highly correlated with the physiological traits by weighted correlation network analysis (WGCNA) analysis. The DEGs encoding antioxidant enzymes, transcription factors, and ion transporters are proposed to confer Cr tolerance in soybean germinating seedlings by reducing the uptake and translocation of Cr, decreasing the level of ROS, and keeping the osmotic balance in soybean germinating seedings. In conclusion, our study provided a molecular regulation network on soybean Cr tolerance at seed germinating stage and identified candidate genes for molecular breeding of low Cr accumulation soybean cultivars.

On-chip generation of Bessel-Gaussian beam via concentrically distributed grating arrays for long-range sensing.

Bessel beam featured with self-healing is essential to the optical sensing applications in the obstacle scattering environment. Integrated on-chip generation of the Bessel beam outperforms the conventional structure by small size, robustness, and alignment-free scheme. However, the maximum propagation distance (Zmax) provided by the existing approaches cannot support long-range sensing, and thus, it restricts its potential applications. In this work, we propose an integrated silicon photonic chip with unique structures featured with concentrically distributed grating arrays to generate the Bessel-Gaussian beam with a long propagation distance. The spot with the Bessel function profile is measured at 10.24 m without optical lenses, and the photonic chip's operation wavelength can be continuously performed from 1500 to 1630 nm. To demonstrate the functionality of the generated Bessel-Gaussian beam, we also experimentally measure the rotation speeds of a spinning object via the rotational Doppler Effect and the distance through the phase laser ranging principle. The maximum error of the rotation speed in this experiment is measured to be 0.05%, indicating the minimum error in the current reports. By the compact size, low cost, and mass production potential of the integrated process, our approach is promising to readily enable the Bessel-Gaussian beam in widespread optical communication and micro-manipulation applications.

Effects of climate change on the geographical distribution and potential distribution areas of 35 Millettia Species in China.

Climate change has an extremely important impact on the geographic distribution of plants. The genus Millettia is an important plant resource in China and is widely used in medicine and ornamental industries. Due to the continuous changes of climate and the development and utilization of plant resources of the genus Millettia, it is of great significance to systematically investigate the geographic distribution of plants of the Millettia and their potential distribution under climate change. DIVA-GIS software was used to analyze 3492 plant specimens of 35 species of genus Millettia in the herbarium, and the ecological geographic distribution and richness of Millettia were analyzed, and the MaxEnt model was used to analyze the current and potential distribution in the future. The results show that the genus Millettia is distributed in 30 provinces in China, among which Yunnan and Guangdong provinces are the most distributed. Our model determines that precipitation in the driest month and annual temperature range are the most important bioclimatic variables. Future climate changes will increase the suitable habitat area of M. congestiflora by 16.75%, but other cliff beans Suitable habitats for vines will decrease significantly: M. cinereal by 47.66%, M. oosperma by 39.16%, M. pulchra by 36.04%, M. oraria by - 29.32%, M. nitida by 22.88%, M. dielsiana by 22.72%, M. sericosema by 19.53%, M. championii by 7.77%, M. pachycarpa by 7.72%, M. speciose by 2.05%, M. reticulata by 1.32%. Therefore, targeted measures should be taken to protect and develop these precious plant resources.

MSN/NA-doped nanoflower enhancing isothermal fluorescent sensor with a portable PCR tube fluorescence reader for the on-site detection of Vibrio parahaemolyticus.

To develop an on-site, thermostatic and rapid sensor for the detection of Vibrio parahaemolyticus (V. parahaemolyticus), A single cross-priming fluorescence (SCPF) sensor was designed using a 3D nano-nucleic acid hybrid material that termed mesoporous silica nanoparticle/nucleic acid-doped nanoflower (MSN/NA-doped nanoflower). In addition, a portable polymerase chain reaction (PCR) tube fluorescence reader was built. Further analysis of the MSN/NA-doped nanoflower morphology and the enhancement mechanism indicated that the MSNs aggregated into larger nanoclusters by adsorbing single cross-priming amplification (sCPA) components, forming MSNs/NAs-doped nanoflowers, and increasing the local concentrations to enhance sCPA efficiency. Cyclic amplification relied mainly on the self-folding hairpin-like structure of the amplified product that continuously formed, opened, re-formed, and opened again. The target DNA was detected with a detection limit of 2.4 copies/µL.

Bifidobacterium animalis subsp. lactis XLTG11 improves antibiotic-related diarrhea by alleviating inflammation, enhancing intestinal barrier function and regulating intestinal flora.

Antibiotic-associated diarrhea (AAD) is a common side effect during antibiotic treatment. In this study, we evaluated the regulatory effect of Bifidobacterium animalis subsp. lactis XLTG11 on mouse diarrhea caused by antibiotic-induced intestinal flora disturbance. Then, two strains of Bifidobacterium animalis subsp. lactis XLTG11 and Bifidobacterium animalis subsp. lactis BB-12 were administered to AAD mice. We found that the recovery effect of using B. lactis XLTG11 was better than that of B. lactis BB-12. B. lactis XLTG11 reduced the pathological characteristics of the intestinal tract, and significantly reduced the levels of lipopolysaccharide (LPS), D-lactic acid (D-LA) and diamine oxidase (DAO) to decrease intestinal permeability. In addition, these two strains significantly increased the expression of aquaporin and tight junction proteins, and inhibited toll-like receptor 4 (TLR4)/activation of the nuclear factor-κB (NF-κB) signaling pathway, significantly increased the levels of anti-inflammatory cytokines and decreased levels of pro-inflammatory cytokines. Moreover, after treatment with B. lactis XLTG11, the contents of acetic acid, propionic acid, butyric acid and total short-chain fatty acids were significantly increased. Compared with the MC group, B. lactis XLTG11 increased the abundance and diversity of the intestinal flora and changed the composition of the intestinal flora. We found that B. lactis XLTG11 can promote the recovery of intestinal flora and mucosal barrier function, thereby effectively improving AAD-related symptoms, providing a scientific basis for future clinical applications.

Protective effect of Amomum Roxb. essential oils in lipopolysaccharide-induced acute lung injury mice and its metabolomics.

ETHNOPHARMACOLOGICAL RELEVANCE: Several Amomum species are commonly used in food as flavoring agents and traditional Chinese medicine to treat inflammation-related diseases. AIM OF THE STUDY: This study aims to investigate the protective effects of Chinese herbal medicines, including six Amomum Roxb. essential oils (AEOs), against acute lung injury (ALI) induced by lipopolysaccharide (LPS) in mice. MATERIALS AND METHODS: The compositions of AEOs were analyzed using gas chromatography - mass spectrometry. RAW264.7 cells were treated with AEOS (0-100 µg/mL) and stimulated with LPS. C57 mice received AEOs (100 mg/kg) via atomization system for seven consecutive days, and then, intratracheal instillation of LPS was applied to establish an in vivo model of acute lung injury. RESULTS: We identified three AEOs demonstrating anti-inflammatory effects and amelioration of LPS-induced lung tissue pathological damage. Furthermore, we found that these AEOs reduced lung wet/dry weight ratios and protein concentrations in the bronchoalveolar lavage fluid of mice with LPS-induced ALI. Additionally, AEOs reduced the levels of malondialdehyde, TNF-α, IL-6, and IL-1ß but increased the levels of superoxide dismutase and catalase in lung tissue, alveolar lavage fluid, and serum samples. We also found that these three AEOs affected proteins related to the TLR4/Myd88/NF-κB pathway. CONCLUSIONS: In summary, our findings revealed that AEOs ameliorate inflammatory and oxidative stress in mice with ALI through the TLR4/Myd88/NF-κB pathway.

Expanding the Coverage of Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches.

Genome-scale metabolomics analysis is increasingly used for pathway and function discovery in the post-genomics era. The great potential offered by developed mass spectrometry (MS)-based technologies has been hindered, since only a small portion of detected metabolites were identifiable so far. To address the critical issue of low identification coverage in metabolomics, we adopted a deep metabolomics analysis strategy by integrating advanced algorithms and expanded reference databases. The experimental reference spectra and in silico reference spectra were adopted to facilitate the structural annotation. To further characterize the structure of metabolites, two approaches were incorporated into our strategy, i.e., structural motif search combined with neutral loss scanning and metabolite association network. Untargeted metabolomics analysis was performed on 150 rice cultivars using ultra-performance liquid chromatography coupled with quadrupole-Orbitrap MS. Consequently, a total of 1939 out of 4491 metabolite features in the MS/MS spectral tag (MS2T) library were annotated, representing an extension of annotation coverage by an order of magnitude in rice. The differential accumulation patterns of flavonoids between indica and japonica cultivars were revealed, especially O-sulfated flavonoids. A series of closely-related flavonolignans were characterized, adding further evidence for the crucial role of tricin-oligolignols in lignification. Our study provides an important protocol for exploring phytochemical diversity in other plant species.

Transcriptome and Metabolome Analysis of a Late-Senescent Vegetable Soybean during Seed Development Provides New Insights into Degradation of Chlorophyll.

(1) Background: Senescence represents the final stage of plant growth and development, which transfers nutrients to growing seeds and directly affects the yield and quality of crops. However, little is known about chlorophyll degradation in developing and maturing seeds, in contrast to leaf senescence; (2) Methods: RNA-Seq was used to analyze the differentially expressed genes of different late-senescent germplasms. A widely untargeted metabolic analysis was used to analyze differential metabolites. In addition, qRT-PCR was conducted to detect gene expression levels; (3) Results: Transcriptome analysis revealed that ZX12 seeds have a higher expression level of the chlorophyll synthesis genes in the early stage of maturity, compared with ZX4, and have a lower expression level of chlorophyll degradation genes in the late stage of maturity. Flavonoids were the primary differential metabolites, and ZX12 contains the unique and highest expression of three types of metabolites, including farrerol-7-O-glucoside, cyanidin-3-o-(6'-o-feruloyl) glucoside, and kaempferide-3-o-(6'-malonyl) glucoside. Among them, farrerol-7-O-glucoside and cyanidin-3-o-(6'-o-feruloyl) glucoside are flavonoid derivatives containing mono and dihydroxy-B-ring chemical structures, respectively; and (4) Conclusions: It is speculated that the two metabolites can slow down the degradation process of chlorophyll by scavenging oxygen-free radicals in the chloroplast.