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Journal articles on the topic 'Transcriptome-metabolome relationships'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Zhu, Chenglin, Sabrina Fasoli, Gloria Isani, and Luca Laghi. "First Insights into the Urinary Metabolome of Captive Giraffes by Proton Nuclear Magnetic Resonance Spectroscopy." Metabolites 10, no. 4 (2020): 157. http://dx.doi.org/10.3390/metabo10040157.

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The urine from 35 giraffes was studied by untargeted 1H-NMR, with the purpose of obtaining, for the first time, a fingerprint of its metabolome. The metabolome, as downstream of the transcriptome and proteome, has been considered as the most representative approach to monitor the relationships between animal physiological features and environment. Thirty-nine molecules were unambiguously quantified, able to give information about diet, proteins digestion, energy generation, and gut-microbial co-metabolism. The samples collected allowed study of the effects of age and sex on the giraffe urinary

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Georgii, Elisabeth, Ming Jin, Jin Zhao, et al. "Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis." BMC Plant Biology 17, no. 1 (2017): 120. https://doi.org/10.1186/s12870-017-1062-y.

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<strong>Background: </strong>Elevated temperature and reduced water availability are frequently linked abiotic stresses that may provoke distinct as well as interacting molecular responses. Based on non-targeted metabolomic and transcriptomic measurements from <i>Arabidopsis</i> rosettes, this study aims at a systematic elucidation of relevant components in different drought and heat scenarios as well as relationships between molecular players of stress response.<strong>Results: </strong>In combined drought-heat stress, the majority of single stress responses are maintained. However, interacti

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Dai, Jiage, Jiabao Cai, Taipeng Zhang, et al. "Transcriptome and Metabolome Analyses Reveal the Mechanism of Corpus Luteum Cyst Formation in Pigs." Genes 14, no. 10 (2023): 1848. http://dx.doi.org/10.3390/genes14101848.

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Corpus luteum cysts are a serious reproductive disorder that affects the reproductive performance of sows. In this study, transcriptome and metabolome datasets of porcine normal and cyst luteal granulosa cells were generated to explore the molecular mechanism of luteal cyst formation. We obtained 28.9 Gb of high−quality transcriptome data from luteum tissue samples and identified 1048 significantly differentially expressed genes between the cyst and normal corpus luteum samples. Most of the differentially expressed genes were involved in cancer and immune signaling pathways. Furthermore, 22,62

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Zhang, Jiahu, Sen Wang, Haibo Wang, et al. "Metabolome and Transcriptome Profiling Reveals the Function of MdSYP121 in the Apple Response to Botryosphaeria dothidea." International Journal of Molecular Sciences 24, no. 22 (2023): 16242. http://dx.doi.org/10.3390/ijms242216242.

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The vesicular transport system is important for substance transport in plants. In recent years, the regulatory relationship between the vesicular transport system and plant disease resistance has received widespread attention; however, the underlying mechanism remains unclear. MdSYP121 is a key protein in the vesicular transport system. The overexpression of MdSYP121 decreased the B. dothidea resistance of apple, while silencing MdSYP121 resulted in the opposite phenotype. A metabolome and transcriptome dataset analysis showed that MdSYP121 regulated apple disease resistance by significantly a

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Wang, Xiaoting, Mingyu Wang, Yongshun Huang, et al. "Genome-Wide Identification and Analysis of Stress Response of Trehalose-6-Phosphate Synthase and Trehalose-6-Phosphate Phosphatase Genes in Quinoa." International Journal of Molecular Sciences 24, no. 8 (2023): 6950. http://dx.doi.org/10.3390/ijms24086950.

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Saline-alkali stress seriously affects the yield and quality of crops, threatening food security and ecological security. Improving saline-alkali land and increasing effective cultivated land are conducive to sustainable agricultural development. Trehalose, a nonreducing disaccharide, is closely related to plant growth and development and stress response. Trehalose 6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) are key enzymes catalyzing trehalose biosynthesis. To elucidate the effects of long-term saline-alkali stress on trehalose synthesis and metabolism, we conducted

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Dong, Zeyu, Shaoguan Zhao, Yizhang Xing, et al. "Time-Series Metabolome and Transcriptome Analyses Reveal the Genetic Basis of Vanillin Biosynthesis in Vanilla." Plants 14, no. 13 (2025): 1922. https://doi.org/10.3390/plants14131922.

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Vanillin, the principal aromatic compound in vanilla, is primarily derived from mature pods of vanilla (Vanilla planifolia Andrews). Although the biosynthetic pathway of vanillin has been progressively elucidated, the specific key enzymes and transcription factors (TFs) governing vanillin biosynthesis require further comprehensive investigation via combining transcriptomic and metabolomic analysis. For this study, V. planifolia (higher vanillin producer) and V. imperialis (lower vanillin producer) were selected. Time-series metabolomics analysis revealed 160–220 days after pollination (DAPs) a

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Xie, Jiahui, Yi Sun, Yue Cao, et al. "Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus." Marine Biotechnology 24, no. 1 (2022): 151–62. http://dx.doi.org/10.1007/s10126-022-10093-4.

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AbstractPolyploid breeding is widely used in aquaculture as an important area of new research. We have previously grown Apostichopus japonicus triploids with a growth advantage. The body length, body weight, and aestivation time of triploid and diploid A. japonicus were measured in this study, and the transcriptome and metabolome were used to examine the growth advantage of triploids A. japonicus. The results showed that the proportion of triploid A. japonicus with a body length of 6–12 cm and 12–18 cm was significantly higher than that of diploid A. japonicus, and triploid A. japonicus had a

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Tang, Meiqiong, Chunying Liang, Yude Peng, et al. "Comparative Transcriptome and Metabolome Analyses Provide New Insights into the Molecular Mechanisms Underlying Taproot Development and Bioactive Compound Biosynthesis in Ficus hirta vahl." Genes 16, no. 7 (2025): 784. https://doi.org/10.3390/genes16070784.

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Background: F. hirta vahl is a famous Chinese medicinal plant. The root is the main organ accumulating bioactive compounds, and its development is directly related to the yield and quality of the harvested F. hirta. However, the molecular mechanisms underlying the bioactive compound biosynthesis occurring during the root development of F. hirta are unknown. Method: Transcriptome and widely targeted metabolome analyses were performed to investigate gene expression and metabolite variation during the development of F. hirta taproots. Results: A total of 3792 differentially expressed genes (DEGs)

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Chen, Lei, Xuesong Wang, Long Cui, et al. "Transcriptome and metabolome analyses reveal anthocyanins pathways associated with fruit color changes in plum (Prunus salicina Lindl.)." PeerJ 10 (December 13, 2022): e14413. http://dx.doi.org/10.7717/peerj.14413.

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Plum (Prunus salicina Lindl.) is one of the most widely cultivated and important fruit trees in temperate and cold regions. Fruit color is a significant trait relating to fruit quality in plum. However, its development mechanism has not been studied from the aspects of transcriptional regulation and metabolomic progress. To reveal the mechanism of fruit color developments in plums, we selected the fruits of two plum cultivars, ‘Changli84’ (Ch84, red fruit) and ‘Dahuangganhe’ (D, yellow fruit) as plant materials for transcriptome sequencing and metabolomic analysis were performed. Based on the

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Han, Danni, Xiaojun Ma, Lei Zhang, et al. "Serial-Omics and Molecular Function Study Provide Novel Insight into Cucumber Variety Improvement." Plants 11, no. 12 (2022): 1609. http://dx.doi.org/10.3390/plants11121609.

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Cucumbers are rich in vitamins and minerals. The cucumber has recently become one of China’s main vegetable crops. More specifically, the adjustment of the Chinese agricultural industry’s structure and rapid economic development have resulted in increases in the planting area allocated to Chinese cucumber varieties and in the number of Chinese cucumber varieties. After complete sequencing of the “Chinese long” genome, the transcriptome, proteome, and metabolome were obtained. Cucumber has a small genome and short growing cycle, and these traits are conducive to the application of molecular bre

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Geddes-McAlister, Jennifer. "Systems Biology in Fungal Research." Journal of Fungi 8, no. 5 (2022): 478. http://dx.doi.org/10.3390/jof8050478.

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The beauty within biological systems can be uncovered using a variety of advanced technological platforms for in-depth profiling. Improvements in genome, transcriptome, proteome, and metabolome investigations, as well as data integration, are moving our understanding of diverse biological systems forward at a rapid rate. Combined with publicly available and customizable bioinformatics tools, we comprehensively profile biological changes under a plethora of circumstances. For fungal pathogens innovation is driven by our ability to explore mechanisms of antifungal resistance, reveal new relation

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Chen, Hongyu, Ying Yu, Jiehong Zhao, and Jian Zhang. "Integrative Transcriptomic and Metabolomic Analysis Reveals Regulatory Networks and Metabolite Dynamics in Gastrodia elata Flower Development." Agronomy 15, no. 2 (2025): 441. https://doi.org/10.3390/agronomy15020441.

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Flower development, a vital phase in the plant life cycle, involves intricate physiological and morphogenetic processes driven by dynamic molecular and metabolic processes. However, the specific molecular mechanisms and metabolite accumulation patterns during Gastrodia elata flower development remain largely unknown. This study utilized Illumina’s next-generation sequencing to analyze the G. elata flower transcriptome across three critical developmental stages, capturing gene expression changes, particularly those related to transcription factors that regulate flower formation and metabolite a

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Cao, Huasheng, Rong Gong, Liang Xiong, et al. "Comparative Metabolome and Transcriptome Analysis Reveals the Possible Roles of Rice Phospholipase A Genes in the Accumulation of Oil in Grains." International Journal of Molecular Sciences 25, no. 21 (2024): 11498. http://dx.doi.org/10.3390/ijms252111498.

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The phospholipase A (PLA) gene family plays a crucial role in the regulation of plant growth, development and stress response. Although PLA genes have been identified in various plant species, their specific functions and characteristics in oil quality formation of rice grains (Oryza sativa L.) have not been studied yet. Here, we identified and characterized 35 rice PLA genes, which were divided into three subgroups based on gene structures and phylogenetic relationships. These genes are distributed unevenly across 11 rice chromosomes. The promoter sequence of rice PLAs contain multiple plant

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Miao, Li, Qinghua Di, Tianshu Sun, et al. "Integrated Metabolome and Transcriptome Analysis Provide Insights into the Effects of Grafting on Fruit Flavor of Cucumber with Different Rootstocks." International Journal of Molecular Sciences 20, no. 14 (2019): 3592. http://dx.doi.org/10.3390/ijms20143592.

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Rootstocks frequently exert detrimental effects on the fruit quality of grafted cucumber (Cucumis sativus L.) plants. To understand and ultimately correct this deficiency, a transcriptomic and metabolomic comparative analysis was performed among cucumber fruits from non-grafted plants (NG), and fruits from plants grafted onto different rootstocks of No.96 and No.45 (Cucurbita moschata. Duch), known to confer a different aroma and taste. We found remarkable changes in the primary metabolites of sugars, organic acids, amino acids, and alcohols in the fruit of the grafted cucumber plants with dif

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Sreenivasulu, Nese, Andreas Graner, and Ulrich Wobus. "Barley Genomics: An Overview." International Journal of Plant Genomics 2008 (March 13, 2008): 1–13. http://dx.doi.org/10.1155/2008/486258.

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Barley (Hordeum vulgare), first domesticated in the Near East, is a well-studied crop in terms of genetics, genomics, and breeding and qualifies as a model plant for Triticeae research. Recent advances made in barley genomics mainly include the following: (i) rapid accumulation of EST sequence data, (ii) growing number of studies on transcriptome, proteome, and metabolome, (iii) new modeling techniques, (iv) availability of genome-wide knockout collections as well as efficient transformation techniques, and (v) the recently started genome sequencing effort. These developments pave the way for

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Wang, Jiyue, Denghong Shi, Yu Bai, et al. "Comprehensive proteomic and metabolomic analysis uncover the response of okra to drought stress." PeerJ 10 (November 23, 2022): e14312. http://dx.doi.org/10.7717/peerj.14312.

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The response of okra to drought stress is very complicated, and the molecular mechanisms underlying this process remains ambiguous up to now. In this study, different degrees of water-stress responses of okra leaf were explained by using transcriptomics and metabolomic approaches. The photosynthesis and glycometabolism in okra leaf were both adversely affected by drought stress, leading to inhibition of the carbohydrate metabolic process, and then influencing the secondary plant metabolism. Further, drought stress disturbed amino acid metabolism, especially for the tyrosine-derived pathway as

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Liu, Yi, Qing Zhu, Zukai Wang, et al. "Integrative Analysis of Transcriptome and Metabolome Reveals the Pivotal Role of the NAM Family Genes in Oncidium hybridum Lodd. Pseudobulb Growth." International Journal of Molecular Sciences 25, no. 19 (2024): 10355. http://dx.doi.org/10.3390/ijms251910355.

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Oncidium hybridum Lodd. is an important ornamental flower that is used as both a cut flower and a potted plant around the world; additionally, its pseudobulbs serve as essential carriers for floral organs and flower development. The NAM gene family is crucial for managing responses to various stresses as well as regulating growth in plants. However, the mechanisms by which NAM genes regulate the development of pseudobulbs remain unclear. In this study, a total of 144 NAM genes harboring complete structural domains were identified in O. hybridum. The 144 NAM genes were systematically classified

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Cao, Jiayu, Jingjing Zeng, Ruoqun Hu, et al. "Comparative Metabolome and Transcriptome Analyses of the Regulatory Mechanism of Light Intensity in the Synthesis of Endogenous Hormones and Anthocyanins in Anoectochilus roxburghii (Wall.) Lindl." Genes 15, no. 8 (2024): 989. http://dx.doi.org/10.3390/genes15080989.

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To explore the regulatory mechanism of endogenous hormones in the synthesis of anthocyanins in Anoectochilus roxburghii (Wall.) Lindl (A. roxburghii) under different light intensities, this study used metabolomics and transcriptomics techniques to identify the key genes and transcription factors involved in anthocyanin biosynthesis. We also analyzed the changes in and correlations between plant endogenous hormones and anthocyanin metabolites under different light intensities. The results indicate that light intensity significantly affects the levels of anthocyanin glycosides and endogenous hor

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Yan, Cunyao, Tao Yang, Baike Wang, Haitao Yang, Juan Wang, and Qinghui Yu. "Genome-Wide Identification of the WD40 Gene Family in Tomato (Solanum lycopersicum L.)." Genes 14, no. 6 (2023): 1273. http://dx.doi.org/10.3390/genes14061273.

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WD40 proteins are a superfamily of regulatory proteins widely found in eukaryotes that play an important role in regulating plant growth and development. However, the systematic identification and characterization of WD40 proteins in tomato (Solanum lycopersicum L.) have not been reported. In the present study, we identified 207 WD40 genes in the tomatoes genome and analyzed their chromosomal location, gene structure and evolutionary relationships. A total of 207 tomato WD40 genes were classified by structural domain and phylogenetic tree analyses into five clusters and 12 subfamilies and were

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Lin, Shuai, Yuqi Liang, Jingqi Geng, Yunfei Yan, Ruipei Ding, and Maozhang He. "Gestational Interrelationships among Gut–Metabolism–Transcriptome in Regulating Early Embryo Implantation and Placental Development in Mice." Microorganisms 12, no. 9 (2024): 1902. http://dx.doi.org/10.3390/microorganisms12091902.

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Decidualization of the uterine endometrium is a critical process for embryo implantation in mammals, primarily occurring on gestational day 8 in pregnant mice. However, the interplay between the maternal gut microbiome, metabolism, and the uterus at this specific time point remains poorly understood. This study employed a multi-omics approach to investigate the metabolic, gut microbiome, and transcriptomic changes associated with early pregnancy (gestational day 8 (E8)) in mice. Serum metabolomics revealed a distinct metabolic profile at E8 compared to controls, with the differential metabolit

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Yang, Mengke, Huanle Li, Haili Qiao, et al. "Integrated Transcriptome and Metabolome Dynamic Analysis of Galls Induced by the Gall Mite Aceria pallida on Lycium barbarum Reveals the Molecular Mechanism Underlying Gall Formation and Development." International Journal of Molecular Sciences 24, no. 12 (2023): 9839. http://dx.doi.org/10.3390/ijms24129839.

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Galls have become the best model for exploring plant–gall inducer relationships, with most studies focusing on gall-inducing insects but few on gall mites. The gall mite Aceria pallida is a major pest of wolfberry, usually inducing galls on its leaves. For a better understanding of gall mite growth and development, the dynamics of the morphological and molecular characteristics and phytohormones of galls induced by A. pallida were studied by histological observation, transcriptomics and metabolomics. The galls developed from cell elongation of the epidermis and cell hyperplasia of mesophylls.

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Li, Nan, Xin Gu, Ming Xin, and Xinpu Wang. "Revealing the Immune Response of Sitona callosus Gyllenhal to Entomopathogenic Fungi Beauveria bassiana Infection Through Integrative Analyses of Transcriptomics and Metabolomics." Insects 15, no. 12 (2024): 940. https://doi.org/10.3390/insects15120940.

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In this study, we selected Sitona callosus, one of the primary insect pests of alfalfa, as the experimental insect and infected it with Beauveria bassiana. Transcriptomic and metabolomic analyses were conducted to explore alterations in gene expression and metabolic processes in S. callosus at 48, 96, and 144 h post infection with B. bassiana. The transcriptomic analysis unveiled that B. bassiana infection boosted immune responses in tubercula, affecting carbohydrate metabolism, cytochrome P450 activity, lysosome function, apoptosis regulation, phagosome formation, glutathione metabolism, amin

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Sun, Jiahong, Xinting Yang, Guiping Zhao, et al. "Protein phosphatase 1 catalytic subunit gamma is a causative gene for meat lightness and redness." PLOS Genetics 20, no. 11 (2024): e1011467. http://dx.doi.org/10.1371/journal.pgen.1011467.

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The quality of meat is important to the consumer. Color is a primary indicator of meat quality and is characterized mainly into lightness, redness, and yellowness. Here, we used the genome-wide association study (GWAS) and gene-based association analysis with whole-genome resequencing of 230 fast-growing white-feathered chickens to map genes related to meat lightness and redness to a 6.24 kb QTL region (Chr15: 6298.34–6304.58 kb). This analysis revealed that only the protein phosphatase 1 catalytic subunit gamma (PPP1CC) was associated with meat color (P = 8.65E-08). The causal relationships b

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Sugawara, Junichi, Daisuke Ochi, Riu Yamashita, et al. "Maternity Log study: a longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy." BMJ Open 9, no. 2 (2019): e025939. http://dx.doi.org/10.1136/bmjopen-2018-025939.

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PurposeA prospective cohort study for pregnant women, the Maternity Log study, was designed to construct a time-course high-resolution reference catalogue of bioinformatic data in pregnancy and explore the associations between genomic and environmental factors and the onset of pregnancy complications, such as hypertensive disorders of pregnancy, gestational diabetes mellitus and preterm labour, using continuous lifestyle monitoring combined with multiomics data on the genome, transcriptome, proteome, metabolome and microbiome.ParticipantsPregnant women were recruited at the timing of first rou

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A. Tamboli, Firoj, Apurva A. Salunkhe, Manasi S. Zade, Monali D Kore, and Rohit A. Mhakle. "Nutrigenomics: A new approach to the diagnosis and prevention of diseases." IP Journal of Nutrition, Metabolism and Health Science 6, no. 4 (2024): 148–56. http://dx.doi.org/10.18231/j.ijnmhs.2023.025.

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An expanding understanding of the ability to alter meals or dietary to enhance health and lower the probability of nutrition-related conditions is what has sparked interest in nutrigenomics. It is a newly developed field which incorporates the areas of bioinformatics, diet, molecular biology, the study of genomes epidemiology, and molecular medicine to reveal the effects of diet on gene activity. More research in this area requires immediate attention to assist people recognize the connection between nutrition and well-being and to make sure all individuals receive advantages from the genomic

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Olsen, Lindsey K., Yuefan Wang, Hui Zhang, Bing Zhang, and Clinical Proteomic Tumor Analysis Consortium (CPTAC). "Abstract 7474: Comprehensive multi-omics characterization of gastric cancers with proteogenomic insights." Cancer Research 85, no. 8_Supplement_1 (2025): 7474. https://doi.org/10.1158/1538-7445.am2025-7474.

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Abstract Gastric cancers are one of the leading causes of cancer-related mortality worldwide. Characterized by high tumor heterogeneity, the treatment of gastric cancers remains challenging. Prior attempts to elucidate the tumor heterogeneity of gastric cancers have included subtyping it into differing clinical and molecular subtypes. For example, the main histological type, adenocarcinoma, has intestinal and diffuse subtypes. At the genomic level, gastric cancers are classified as either Epstein-Barr virus (EBV), microsatellite instability (MSI), chromosomal instability (CIN), or genomically

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Xue, Jiarui, Fenglin Dong, Yiwei Liu, et al. "Role of BAZ2A in Cervical Cancer and Its Effect on Tumor Cell Metabolism." Advances in World Medical Research 1, no. 1 (2025): 3–17. https://doi.org/10.71204/j7y2f615.

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This study aims to investigate the role of BAZ2A in cervical cancer and its relationship with cancer development and glycolipid metabolism. BAZ2A knockdown experiments were performed in HeLa cells to study its effects on cell proliferation, invasion, cloning and migration; transcriptome and metabolome sequencing were also performed, and differentially expressed genes and metabolites were analyzed by GO and KEGG enrichment, etc. BAZ2A is highly expressed in cervical cancer, and the knockdown of BAZ2A inhibits the related malignant behaviors in HeLa cells. Transcriptome analysis identified a lar

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Ji, Xiaolong, Jing Ren, Shaoyu Lang, Di Wang, Liwei Zhu, and Xingshun Song. "Differential Regulation of Anthocyanins in Cerasus humilis Fruit Color Revealed by Combined Transcriptome and Metabolome Analysis." Forests 11, no. 10 (2020): 1065. http://dx.doi.org/10.3390/f11101065.

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Coloring is an important appearance quality of fruit. In order to evaluate the relationship between metabolites and fruit color, we analyzed the metabolites and transcriptional profiles of two different Cerasus humilis cultivars: “RF” (cv. Zhangwu, red fruit) and “YF” (cv. Nongda No.5, yellow fruit). The results of identification and quantification of metabolites showed that there were significant differences in the contents of 11 metabolites between RF and YF. Transcriptomics was used to analyze the expression patterns of genes related to the anthocyanin biosynthesis pathway, and subsequently

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Jiang, Susu, Guohua Zhang, Jian Miao, et al. "Transcriptome and Metabolome Analyses Provide Insight into the Glucose-Induced Adipogenesis in Porcine Adipocytes." Current Issues in Molecular Biology 46, no. 3 (2024): 2027–42. http://dx.doi.org/10.3390/cimb46030131.

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Glucose is a major energy substrate for porcine adipocytes and also serves as a regulatory signal for adipogenesis and lipid metabolism. In this study, we combined transcriptome and metabolome analyses to reveal the underlying regulatory mechanisms of high glucose (HG) on adipogenesis by comparing differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) identified in porcine adipocytes. Results showed that HG (20 mmol/L) significantly increased fat accumulation in porcine adipocytes compared to low glucose (LG, 5 mmol/L). A total of 843 DEGs and 365 DAMs were ide

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Liu, Yongjiang, Junna Liu, Li Li, Ping Zhang, Qianchao Wang, and Peng Qin. "Transcriptome and Metabolome Combined to Analyze Quinoa Grain Quality Differences of Different Colors Cultivars." International Journal of Molecular Sciences 23, no. 21 (2022): 12883. http://dx.doi.org/10.3390/ijms232112883.

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Quinoa (Chenopodium quinoa Wild.) has attracted considerable attention owing to its unique nutritional, economic, and medicinal values. Meanwhile, quinoa germplasm resources and grain colors are rich and diverse. In this study, we analyzed the composition of primary and secondary metabolites and the content of the grains of four different high-yield quinoa cultivars (black, red, white, and yellow) harvested 42 days after flowering. The grains were subjected to ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and transcriptome sequencing to identify the differential

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Hao, Zhilong, Yanping Tan, Jiao Feng, et al. "Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves (Camellia sinensis) post-harvest." PeerJ 11 (February 8, 2023): e14869. http://dx.doi.org/10.7717/peerj.14869.

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Sugar metabolites not only act as the key compounds in tea plant response to stress but are also critical for tea quality formation during the post-harvest processing of tea leaves. However, the mechanisms by which sugar metabolites in post-harvest tea leaves respond to mechanical stress are unclear. In this study, we aimed to investigate the effects of mechanical stress on saccharide metabolites and related post-harvest tea genes. Withered (C15) and mechanically-stressed (V15) for 15 min Oolong tea leaves were used for metabolome and transcriptome sequencing analyses. We identified a total of

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Nangia-Makker, Pratima, Madison Ahrens, Neeraja Purandare, et al. "Inter-Relationship Between Melanoma Vemurafenib Tolerance Thresholds and Metabolic Pathway Choice." Cells 14, no. 12 (2025): 923. https://doi.org/10.3390/cells14120923.

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Melanomas quickly acquire resistance to vemurafenib, an important therapeutic for BRAFV600 mutant melanomas. Although combating vemurafenib resistance (VemR) to counter mitochondrial metabolic shift using mitochondria-targeting therapies has promise, no studies have analyzed the relationship between vemurafenib tolerance levels and metabolic plasticity. To determine how vemurafenib endurance levels drive metabolic plasticity, we developed isogenic BRAFV600E VemR melanoma models with variant vemurafenib tolerances and performed an integrative analysis of metabolomic and transcriptome alteration

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Liu, Chang, Jie Pan, Zhi-Gang Yin, et al. "Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia." PeerJ 10 (June 29, 2022): e13670. http://dx.doi.org/10.7717/peerj.13670.

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Background Radix Ardisia (Jab Bik Lik Jib) is a common Miao medicine and is widely distributed in the Guizhou region of southern China. The botanical origin of Radix Ardisia includes the dry root and rhizome of Ardisia Crenata Sims (ACS) or Ardisia Crispa (Thunb.) A.DC. (AC), which are closely related species morphologically. However, the secondary metabolites in their roots are different from one another, especially the flavonoids, and these differences have not been thoroughly explored at the molecular level. This project preliminarily identified regulatory molecular mechanisms in the biosyn

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Xiong, Yun, Junya He, Mingzhang Li, et al. "Integrative Analysis of Metabolome and Transcriptome Reveals the Mechanism of Color Formation in Yellow-Fleshed Kiwifruit." International Journal of Molecular Sciences 24, no. 2 (2023): 1573. http://dx.doi.org/10.3390/ijms24021573.

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During the development of yellow-fleshed kiwifruit (Actinidia chinensis), the flesh appeared light pink at the initial stage, the pink faded at the fastest growth stage, and gradually changed into green. At the maturity stage, it showed bright yellow. In order to analyze the mechanism of flesh color change at the metabolic and gene transcription level, the relationship between color and changes of metabolites and key enzyme genes was studied. In this study, five time points (20 d, 58 d, 97 d, 136 d, and 175 d) of yellow-fleshed kiwifruit were used for flavonoid metabolites detection and transc

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Hou, Jiaqi, Yuhan Zhou, Liping Ran, et al. "Transcriptome and Metabolome Analysis Reveal the Flavonoid Biosynthesis Mechanism of Abelmoschus manihot L. at Different Anthesis Stages." Metabolites 13, no. 2 (2023): 216. http://dx.doi.org/10.3390/metabo13020216.

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Abelmoschus manihot L. (HSK) is a rare and endangered species in the wild that grows on the cliffs of deep mountains. As a natural plant, the chemical composition of HSK is relatively complex, which mainly includes flavonoids, organic acids, polysaccharides, and various trace elements with good effects of clearing away heat, anti-inflammatory, analgesic, and calming nerves, and inhibiting tumor cells. In this experiment, different developmental stages of HSK flowers were used for optimization of the flavonoid extraction and determining method. The antioxidant activities, flavonoid accumulation

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Crispo, Fabiana, Valentina Condelli, Silvia Lepore, et al. "Metabolic Dysregulations and Epigenetics: A Bidirectional Interplay that Drives Tumor Progression." Cells 8, no. 8 (2019): 798. http://dx.doi.org/10.3390/cells8080798.

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Cancer has been considered, for a long time, a genetic disease where mutations in key regulatory genes drive tumor initiation, growth, metastasis, and drug resistance. Instead, the advent of high-throughput technologies has revolutionized cancer research, allowing to investigate molecular alterations at multiple levels, including genome, epigenome, transcriptome, proteome, and metabolome and showing the multifaceted aspects of this disease. The multi-omics approaches revealed an intricate molecular landscape where different cellular functions are interconnected and cooperatively contribute to

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Zhang, Ying, Yuanyuan Li, and Shunxing Guo. "Effects of the mycorrhizal fungus Ceratobasidium sp. AR2 on growth and flavonoid accumulation in Anoectochilus roxburghii." PeerJ 8 (January 16, 2020): e8346. http://dx.doi.org/10.7717/peerj.8346.

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Background Anoectochilus roxburghii is a traditional Chinese medicine with potent medicinal activity owing to the presence of secondary metabolites, particularly flavonoids. A. roxburghii also maintains a symbiotic relationship with mycorrhizal fungi. Moreover, mycorrhizal fungi can induce metabolite synthesis in host plants. However, little is known about the role of mycorrhizal fungi in promoting the accumulation of flavonoid metabolites in A. roxburghii. Methods A. roxburghii and the isolated fungus Ceratobasidium sp. AR2 were cocultured. The portion of A. roxburghii above the medium treate

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Jiang, Shizheng, Juxian Guo, Imran Khan, et al. "Comparative Metabolome and Transcriptome Analyses Reveal the Regulatory Mechanism of Purple Leafstalk Production in Taro (Colocasia esculenta L. Schott)." Genes 15, no. 1 (2024): 138. http://dx.doi.org/10.3390/genes15010138.

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Taro is a plant in the Araceae family, and its leafstalk possesses significant botanical and culinary value owing to its noteworthy medicinal and nutritional attributes. Leafstalk colour is an essential attribute that significantly influences its desirability and appeal to both breeders and consumers. However, limited information is available about the underlying mechanism responsible for the taro plant’s colouration. Thus, the purpose of the current study was to elucidate the information on purple leafstalks in taro through comprehensive metabolome and transcriptome analysis. In total, 187 fl

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Wu, Shumei, Yue Gao, Qi Zhang, Fen Liu, and Weiming Hu. "Application of Multi-Omics Technologies to the Study of Phytochromes in Plants." Antioxidants 13, no. 1 (2024): 99. http://dx.doi.org/10.3390/antiox13010099.

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Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-d

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Fu, Baochun, and Yongqiang Tian. "Combined Study of Transcriptome and Metabolome Reveals Involvement of Metabolites and Candidate Genes in Flavonoid Biosynthesis in Prunus avium L." Horticulturae 9, no. 4 (2023): 463. http://dx.doi.org/10.3390/horticulturae9040463.

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Sweet cherry (Prunus avium L.) is a popular fruit tree grown for its juicy fruit and pleasing appearance. The fruit pf the sweet cherry contains active antioxidants and other chemical compounds essential for human health. For this study, we performed the transcriptomics and metabolomics analysis using young Green Peel (GP) and mature Red Peel (RP) from sweet cherries to understand the underlying genetic mechanism regulating fruit development and ripening. Using high-throughput RNA sequencing and ultra-performance liquid chromatography, with quadrupole time-of-flight tandem mass spectrometry, r

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Zhang, Wangshu, Yue Xu, Luyang Jing, Baoxin Jiang, Qinghao Wang, and Yuxi Wang. "Preliminary Study on the Formation Mechanism of Malformed Sweet Cherry (Prunus avium L.) Fruits in Southern China Using Transcriptome and Metabolome Data." International Journal of Molecular Sciences 25, no. 1 (2023): 153. http://dx.doi.org/10.3390/ijms25010153.

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Gibberellin (GA) is an important plant hormone that is involved in various physiological processes during plant development. Sweet cherries planted in southern China have always encountered difficulty in bearing fruit. In recent years, gibberellin has successfully solved this problem, but there has also been an increase in malformed fruits. This study mainly explores the mechanism of malformed fruit formation in sweet cherries. By analyzing the synthesis pathway of gibberellin using metabolomics and transcriptomics, the relationship between gibberellin and the formation mechanism of deformed f

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Wang, Xingbin, Sitian Li, Xiao Zhang, et al. "Integration of Transcriptome and Metabolome Reveals Wax Serves a Key Role in Preventing Leaf Water Loss in Goji (Lycium barbarum)." International Journal of Molecular Sciences 25, no. 20 (2024): 10939. http://dx.doi.org/10.3390/ijms252010939.

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Drought stress is one of the main abiotic stresses that limit plant growth and affect fruit quality and yield. Plants primarily lose water through leaf transpiration, and wax effectively reduces the rate of water loss from the leaves. However, the relationship between water loss and the wax formation mechanism in goji (Lycium barbarum) leaves remains unclear. ‘Ningqi I’ goji and ‘Huangguo’ goji are two common varieties. In this study, ‘Ningqi I’ goji and ‘Huangguo’ goji were used as samples of leaf material to detect the differences in the water loss rate, chlorophyll leaching rate, wax phenot

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Wang, Chao, Rong Huang, Jianfeng Wang, et al. "Comprehensive Analysis of Transcriptome and Metabolome Elucidates the Molecular Regulatory Mechanism of Salt Resistance in Roots of Achnatherum inebrians Mediated by Epichloë gansuensis." Journal of Fungi 8, no. 10 (2022): 1092. http://dx.doi.org/10.3390/jof8101092.

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Salinization of soil is a major environmental risk factor to plant functions, leading to a reduction of productivity of crops and forage. Epichloë gansuensis, seed-borne endophytic fungi, establishes a mutualistic symbiotic relationship with Achnatherum inebrians and confers salt tolerance in the host plants. In this study, analysis of transcriptome and metabolome was used to explore the potential molecular mechanism underlying the salt-adaptation of A. inebrians roots mediated by E. gansuensis. We found that E. gansuensis played an important role in the gene expression of the host’s roots and

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Shen, Fei, Guang Wang, and Shijiang Zhu. "The Role of Aspergillus niger in Regulating Internal Browning Involves Flavonoid Biosynthesis and the Endophytic Fungal Community of Pineapple." Journal of Fungi 10, no. 11 (2024): 794. http://dx.doi.org/10.3390/jof10110794.

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Endophytic fungi are commonly used to control plant diseases, overcoming the drawbacks of chemical agents. The internal browning (IB) of postharvest pineapple fruit, a physiological disease, leads to quality losses and limits industrial development. This work investigated the relationship among the effects of Aspergillus niger (An) on IB controlling, flavonoid metabolism and the endophytic fungal community of pineapple through metabolomics, transcriptomics, microbiomics and microorganism mutagenesis technology. We obtained an endophyte An that can control the IB of pineapple and screened its m

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Ohara, Yuuki, Wei Tang, Liu Huaitian, et al. "Abstract 6225: SERPINB3 promotes the aggressive basal-like/squamous subtype and correlates with poor prognosis in pancreatic ductal adenocarcinoma through metabolic reprogramming." Cancer Research 83, no. 7_Supplement (2023): 6225. http://dx.doi.org/10.1158/1538-7445.am2023-6225.

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Abstract In this study, we aimed to find genes with a key function in the development of molecular subtypes in pancreatic ductal adenocarcinoma (PDAC). Through transcriptome analysis, we discovered that the endogenous serine/cysteine proteinase inhibitor SERPINB3 (squamous cell carcinoma antigen 1, SCCA1) was distinctively upregulated in the basal-like/squamous subtype, known as an aggressive subtype, and this upregulation associated with decreased patient survival in both a test (N=123) and a validation cohort (N=84). In additional investigations of the tumor metabolome and transcriptome usin

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Zhou, H., T. Wu, F. Wang, et al. "P135 Mixed probiotics containing Bifidobacterium longum and its metabolites inhibit the formation of NLRP3 inflammasomes by suppressing GBP5 expression in macrophages in ulcerative colitis." Journal of Crohn's and Colitis 18, Supplement_1 (2024): i429—i430. http://dx.doi.org/10.1093/ecco-jcc/jjad212.0265.

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Abstract Background Ulcerative Colitis (UC) is a non-specific chronic inflammation of the intestine. As an intestinal disease with a gradually increasing incidence in recent years and increasingly valued by medical staff, UC has a close relationship with intestinal flora. At present, domestic and foreign guidelines point out that probiotics can be used to induce remission in ulcerative colitis, but there are no clear instructions on the selection of probiotics, the use of dosage forms, and the dosage of probiotics, and there is a lack of relevant clinical and basic research. This study aims to

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Gao, Yan, Xuan Dong, Rongjin Wang, et al. "Exogenous Calcium Alleviates Oxidative Stress Caused by Salt Stress in Peanut Seedling Roots by Regulating the Antioxidant Enzyme System and Flavonoid Biosynthesis." Antioxidants 13, no. 2 (2024): 233. http://dx.doi.org/10.3390/antiox13020233.

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Soil salinity is one of the adversity stresses plants face, and antioxidant defense mechanisms play an essential role in plant resistance. We investigated the effects of exogenous calcium on the antioxidant defense system in peanut seedling roots that are under salt stress by using indices including the transcriptome and absolute quantitative metabolome of flavonoids. Under salt stress conditions, the antioxidant defense capacity of enzymatic systems was weakened and the antioxidant capacity of the linked AsA-GSH cycle was effectively inhibited. In contrast, the ascorbate biosynthesis pathway

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Liu, Lu, Qi Wang, Linfeng Zhu, Huiming Guo, Hongmei Cheng, and Xiaofeng Su. "Heat Shock Transcription Factor GhHSFB2a Is Crucial for Cotton Resistance to Verticillium dahliae." International Journal of Molecular Sciences 24, no. 3 (2023): 1845. http://dx.doi.org/10.3390/ijms24031845.

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Heat shock transcription factors (HSFs) play a critical regulatory role in many plant disease resistance pathways. However, the molecular mechanisms of cotton HSFs involved in resistance to the soil-borne fungus Verticillium dahliae are limited. In our previous study, we identified numerous differentially expressed genes (DEGs) in the transcriptome and metabolome of V. dahliae-inoculated Arabidopsis thaliana. In this study, we identified and functionally characterized GhHSFB2a, which is a DEG belonging to HSFs and related to cotton immunity to V. dahliae. Subsequently, the phylogenetic tree of

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Gan, Xiaolong, Xuemei Bao, Baolong Liu, et al. "Chemical Constituents and Molecular Mechanism of the Yellow Phenotype of Yellow Mushroom (Floccularia luteovirens)." Journal of Fungi 8, no. 3 (2022): 314. http://dx.doi.org/10.3390/jof8030314.

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(1) Background: Yellow mushroom (Floccularia luteovirens) is a natural resource that is highly nutritional, has a high economic value, and is found in Northwest China. Despite its value, the chemical and molecular mechanisms of yellow phenotype formation are still unclear. (2) Methods: This study uses the combined analysis of transcriptome and metabolome to explain the molecular mechanism of the formation of yellow mushroom. Subcellular localization and transgene overexpression techniques were used to verify the function of the candidate gene. (3) Results: 112 compounds had a higher expression

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Ma, Shengchao, Dan Wang, Menghua Zhang, et al. "Transcriptomic and Metabolomics Joint Analyses Reveal the Influence of Gene and Metabolite Expression in Blood on the Lactation Performance of Dual-Purpose Cattle (Bos taurus)." International Journal of Molecular Sciences 25, no. 22 (2024): 12375. http://dx.doi.org/10.3390/ijms252212375.

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Blood is an important component for maintaining animal lives and synthesizing sugars, lipids, and proteins in organs. Revealing the relationship between genes and metabolite expression and milk somatic cell count (SCC), milk fat percentage, milk protein percentage, and lactose percentage in blood is helpful for understanding the molecular regulation mechanism of milk formation. Therefore, we separated the buffy coat and plasma from the blood of Xinjiang Brown cattle (XJBC) and Chinese Simmental cattle (CSC), which exhibit high and low SCC/milk fat percentage/milk protein percentage/lactose per

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