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Keywords = WGCNA(Weighted Gene Co-expression Network Analysis) analysis

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18 pages, 3532 KiB  
Article
Transcriptomic Profiling of Paulownia fortunei (Seem.) Hemsl. Roots in Response to Chromium and Copper Stress
by Jiang Su, Xinfeng Pan, Kanghua Xian, Chuanming Fu, Jinxiang He, Baojun Liu, Jinhan Sang and Ningzhen Huang
Genes 2025, 16(5), 595; https://doi.org/10.3390/genes16050595 (registering DOI) - 18 May 2025
Abstract
Background: Soil heavy metal pollution by chromium (Cr) and copper (Cu) is a global environmental concern. Methods: This study evaluated Cr/Cu accumulation in Paulownia fortunei tissues and analyzed its root transcriptome under Cr and Cu stress to elucidate molecular response mechanisms. Results: Findings [...] Read more.
Background: Soil heavy metal pollution by chromium (Cr) and copper (Cu) is a global environmental concern. Methods: This study evaluated Cr/Cu accumulation in Paulownia fortunei tissues and analyzed its root transcriptome under Cr and Cu stress to elucidate molecular response mechanisms. Results: Findings revealed significantly higher Cr and Cu accumulation capacity in roots compared to stems and leaves. Transcriptome sequencing identified 6017 and 2265 differentially expressed genes (DEGs) under Cr and Cu stress, respectively. These DEGs were primarily involved in redox reactions, stress responses, transcriptional regulation, transmembrane transport, and metabolism. Quantitative PCR of 20 selected genes validated dynamic expression changes under stress. Weighted Gene Co-expression Network Analysis (WGCNA) identified distinct co-expression modules associated with Cr and Cu. Hub gene analysis implicated Pfo_020668 and Pfo_019190 in Cr response, while Pfo_010312 and Pfo_000197 may enhance Cu tolerance via cell wall polysaccharide synthesis regulation. Pathways related to pyruvate metabolism and proteasome were significantly enriched under Cr stress, whereas amino acid metabolism pathways were prominent under Cu stress. Conclusions: Differentially expressed transporter genes suggest potential roles in heavy metal uptake and transport. This transcriptomic analysis provides novel insights into P. fortunei’s molecular responses to Cr and Cu stress, offering a foundation for utilizing this species in soil phytoremediation efforts. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)
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16 pages, 2493 KiB  
Article
Comparative Transcriptome Analysis of Susceptible and Resistant Rutaceae Plants to Huanglongbing
by Huihong Liao, Fuping Liu, Xi Wang, Hongming Huang, Qichun Huang, Nina Wang and Chizhang Wei
Agronomy 2025, 15(5), 1218; https://doi.org/10.3390/agronomy15051218 - 17 May 2025
Viewed by 52
Abstract
Huanglongbing (HLB), also known as citrus greening, is a devastating disease affecting the citrus industry worldwide. This study aimed to investigate the transcriptional responses of two Rutaceae species, Ponkan Mandarin (susceptible) and Punctate Wampee (resistant), to HLB infection. Comparative transcriptome analysis was conducted [...] Read more.
Huanglongbing (HLB), also known as citrus greening, is a devastating disease affecting the citrus industry worldwide. This study aimed to investigate the transcriptional responses of two Rutaceae species, Ponkan Mandarin (susceptible) and Punctate Wampee (resistant), to HLB infection. Comparative transcriptome analysis was conducted to identify differentially expressed genes (DEGs) and pathways involved in defense mechanisms. The transcriptome data showed that in the susceptible Ponkan Mandarin, there were 1519 upregulated genes and 700 downregulated genes, while in the resistant Punctate Wampee variety, there were 1611 upregulated genes and 1727 downregulated genes. Upon infection, 297 genes were upregulated in both varieties, while 211 genes were downregulated in both. These genes included transcription factors from different families such as WRKY, ERF, and MYB. Ponkan Mandarin primarily relies on pathways like lignin synthesis and cell wall modification to defend against HLB, whereas Punctate Wampee mainly resists HLB by regulating cellular homeostasis and metabolism. Weighted Gene Co-expression Network Analysis (WGCNA) identified ten potential key resistance genes in the resistant Punctate Wampee variety, including genes involved in lignin biosynthesis and genes related to cellular signaling pathways. These findings not only enhance our understanding of the distinct defense mechanisms employed by citrus species against HLB infection but also offer novel perspectives for developing effective prevention and management strategies against this disease. Full article
(This article belongs to the Special Issue Resistance-Related Gene Mining and Genetic Improvement in Crops)
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19 pages, 3886 KiB  
Article
Hippocampal Transcriptome Analysis in a Mouse Model of Chronic Unpredictable Stress Insomnia
by Shuo Zhang, Changqing Tong, Na Cao, Dong Tian, Linshan Du, Ya Xu, Weiguang Wang, Zijie Chen and Shuangqing Zhai
Biomedicines 2025, 13(5), 1205; https://doi.org/10.3390/biomedicines13051205 - 15 May 2025
Viewed by 71
Abstract
Background: This study aimed to develop a model for understanding stress-induced sleep disturbances and to explore the potential interactions between sleep disturbances and mood disturbances. Methods: The chronic unpredictable mild stress (CUMS) group was established using the CUMS method, while the [...] Read more.
Background: This study aimed to develop a model for understanding stress-induced sleep disturbances and to explore the potential interactions between sleep disturbances and mood disturbances. Methods: The chronic unpredictable mild stress (CUMS) group was established using the CUMS method, while the CUMS+Noise group was subjected to an additional 8-h exposure to noise in conjunction with the CUMS protocol. Each group was tested for anxiety and depressive-like behavior using the open-field, elevated plus maze, tail suspension, and forced swimming tests in male C57BL/6J mice. Subsequently, we assessed sleep status using sleep recordings and a standardized scoring system alongside the pentobarbital sodium-induced sleep test. Results: The mice in both model groups exhibited anxiety-like behavior. Sleep disturbances observed in the CUMS+Noise group were characterized by disruptions in sleep duration and circadian rhythm. This observation was supported by a marked reduction in multiple sleep time intervals and single sleep duration, as well as a significant increase in sleep duration at the final time interval of ZT23-24. To further investigate the potential mechanisms of interaction, we conducted an analysis of hub genes present in the hippocampal sequencing data utilizing weighted gene co-expression network analysis (WGCNA). Pearson correlation analysis revealed a significant association between the hub genes Alb, P2rx1, and Npsr1 and key phenotypic traits. However, PCR experiments indicated that only Alb showed a significant difference, which aligns with the sequencing results. Conclusions: Albumin is a crucial transporter protein for thyroid hormones and plays a vital role in their metabolism. The interaction between sleep disorders and anxiety-like behavior may be closely linked to the dysfunctional transportation of thyroid hormones by albumin. Full article
(This article belongs to the Section Neurobiology and Clinical Neuroscience)
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18 pages, 5494 KiB  
Article
Transcriptomic Profiling Uncovers Molecular Basis for Sugar and Acid Metabolism in Two Pomegranate (Punica granatum) Varieties
by Ding Ke, Yilong Zhang, Yingfen Teng and Xueqing Zhao
Foods 2025, 14(10), 1755; https://doi.org/10.3390/foods14101755 - 15 May 2025
Viewed by 133
Abstract
Soluble sugars and organic acids constitute the primary flavor determinants in fruits and elucidating their metabolic mechanisms provides crucial theoretical foundations for fruit breeding practices and food industry development. Through integrated physiological and transcriptomic analysis of pomegranate varieties ‘Sharp Velvet’ with high acid [...] Read more.
Soluble sugars and organic acids constitute the primary flavor determinants in fruits and elucidating their metabolic mechanisms provides crucial theoretical foundations for fruit breeding practices and food industry development. Through integrated physiological and transcriptomic analysis of pomegranate varieties ‘Sharp Velvet’ with high acid content and ‘Azadi’ with low acid content, this study demonstrated that the differences in flavor between the two varieties were mainly caused by differences in citric acid content rather than in soluble sugar content. Transcriptome profiling identified 11 candidate genes involved in sugar and acid metabolism, including three genes associated with soluble sugar metabolism (FBA1, SS, and SWEET16) and eight genes linked to organic acid metabolism (ADH1, GABP1, GABP2, GABP3, GABP4, ICL, ME1, and PDC4). These data indicated that differences in citric acid content between the two varieties mainly stemmed from differences in the regulation of the citric acid degradation pathway, which relies mainly on the γ-aminobutyric acid (GABA) branch rather than the isocitric acid lyase (ICL) pathway. Citric acid accumulation in pomegranate fruit was driven by metabolic fluxes rather than vesicular storage capacity. Weighted gene co-expression network analysis (WGCNA) uncovered a significant citric acid content associated module (r = −0.72) and predicted six core transcriptional regulators (bHLH42, ERF4, ERF062, WRKY6, WRKY23, and WRKY28) within this network. Notably, bHLH42, ERF4, and WRKY28 showed significant positive correlations with citric acid content, whereas ERF062, WRKY6, and WRKY23 demonstrated significant negative correlations. Our findings provide comprehensive insights into the genetic architecture governing soluble sugars and organic acids homeostasis in pomegranate, offering both a novel mechanistic understanding of fruit acidity regulation and valuable molecular targets for precision breeding of fruit quality traits. Full article
(This article belongs to the Special Issue Foodomics Approaches—Technologies and Their Applications)
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19 pages, 4871 KiB  
Article
The Identification of Regulatory Genes Involved in Light-Induced Anthocyanin Accumulation in Aft Tomato Developing Fruits
by Jiazhen Li, Ji Li, Rui Su, Haifang Yan, Fei Zhao, Qijiang Xu and Bo Zhou
Horticulturae 2025, 11(5), 535; https://doi.org/10.3390/horticulturae11050535 - 15 May 2025
Viewed by 161
Abstract
Anthocyanins, which accumulate in fruits, flowers, and vegetative organs, play a critical role in plant reproduction, disease resistance, stress tolerance, and promoting human health. Although light significantly influences the development of various fruit pigments, the specific mechanisms through which it regulates anthocyanin accumulation [...] Read more.
Anthocyanins, which accumulate in fruits, flowers, and vegetative organs, play a critical role in plant reproduction, disease resistance, stress tolerance, and promoting human health. Although light significantly influences the development of various fruit pigments, the specific mechanisms through which it regulates anthocyanin accumulation during fruit ripening are not yet fully understood. This study aimed to investigate the role of light in anthocyanin biosynthesis using Aft tomato fruits, which accumulate pigments in the epidermis. To explore the effects of light on anthocyanin biosynthesis, half of each fruit was covered with aluminum foil to establish light-exposed and bagged conditions for comparative analysis. The results showed that the bagged treatment led to a significant decrease in the total anthocyanin content of the fruits. Transcriptome analysis revealed a notable upregulation of several structural genes involved in the anthocyanin biosynthetic pathway, specifically Sl4CL, SlCHS, SlCHI, SlF3H, SlDFR, and Sl3GT in the light-exposed fruits. Additionally, the expression levels of light-responsive genes and transcription factors, such as SlCRY1, SlSPA, SlUVR3, SlHY5, SlBBX24, SlMYB11, MADS-box transcription factor 23, SlHD-ZIP I/II, SlAN2-like, SlbHLH and SlWD40 proteins, were significantly higher in the light-exposed samples compared to those subjected to the bagged treatment. Weighted Gene Co-Expression Network Analysis (WGCNA) demonstrated a strong association between light-induced gene expression such as SlPAL, SlCHS1, SlDFR, SlF3H, SlF3′5′H, SlANS, SlHY5, and SlAN2-like quantified by qRT-PCR analysis and anthocyanin biosynthesis. Moreover, as the fruit matured, both anthocyanin accumulation and the expression of genes related to its biosynthetic pathway increased. These findings contribute to a foundational understanding of the regulatory network that influences light-induced processes and fruit development impacting anthocyanin accumulation, which will facilitate in-depth study of the functions of these identified genes and provide a foundation for breeding anthocyanin-rich tomato varieties. Full article
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15 pages, 12467 KiB  
Article
Deciphering the Transcriptomic Complexity of Yak Skin Across Different Ages and Body Sites
by Xiaolan Zhang, Bingang Shi, Zhidong Zhao, Yunqi Deng, Xuelan Zhou and Jiang Hu
Int. J. Mol. Sci. 2025, 26(10), 4601; https://doi.org/10.3390/ijms26104601 - 11 May 2025
Viewed by 213
Abstract
Differences in skin and hair phenotypes between the scapular and ventral regions of yaks (Bos grunniens) are obvious and become more prominent with age. However, the genetic mechanism that causes differences in yak skin at different ages has not been reported. In this [...] Read more.
Differences in skin and hair phenotypes between the scapular and ventral regions of yaks (Bos grunniens) are obvious and become more prominent with age. However, the genetic mechanism that causes differences in yak skin at different ages has not been reported. In this study, we investigated the transcriptomic profile of yak skin across different ages (0.5 years, 2.5 years, and 4.5 years) and body sites (scapular and ventral regions). Differential gene expression analysis was initially conducted to explore the transcriptomic differences in skin at different ages and different body sites. Subsequently, weighted gene co-expression network analysis (WGCNA) was employed to analyze the transcriptomic data comprehensively. The results showed that, among all comparison groups, the Y2.5_S vs. Y2.5_V group (regional comparison) exhibited the highest number of DEGs, with 491 genes (179 upregulated and 312 downregulated), followed by the Y2.5_V vs. Y0.5_V group (age comparison), which had 370 DEGs (103 upregulated and 267 downregulated). DEGs such as IGF2BP3, ADCY8, FOSL1, and S100A8 were found in all comparison groups of different ages, and multiple members of the HOX gene family including HOXC10, HOXA9, HOXA6, HOXB9, and HOXB6 were differentially expressed in comparison groups at different sites. Functional enrichment analysis showed that there were more obvious differences in immune function between different ages of skin and more obvious differences in endocrine function between different parts of skin. WGCNA revealed that genes related with immunity such as GLYATL2, ACSL5, and SPDEF were the core genes of the co-expression module associated with the scapula region, and multiple genes related to hair follicle development such as FOXN1, OVOL1, DLX3, HOXC13, and TCHH were found to be the hub genes of the co-expression module associated with the ventral region. Overall, our study provides valuable insights into the transcriptomic complexity of yak skin across different ages and body sites. The differential gene expression patterns and co-expression network modules identified in this study lay the foundation for further research on skin biology and adaptation mechanisms in yaks. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 3306 KiB  
Article
Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples
by Wenyuan Yang, Hang Yu, Lian Tao and Hongjiang Xie
Curr. Issues Mol. Biol. 2025, 47(5), 341; https://doi.org/10.3390/cimb47050341 - 8 May 2025
Viewed by 287
Abstract
Low-acid apples are popular among consumers, but the mechanisms behind the complex differences in acidity among varieties that are caused by high altitude are not clear. In this study, we used the ‘Golden Delicious’ apple and its superior variant in the Western Sichuan [...] Read more.
Low-acid apples are popular among consumers, but the mechanisms behind the complex differences in acidity among varieties that are caused by high altitude are not clear. In this study, we used the ‘Golden Delicious’ apple and its superior variant in the Western Sichuan Plateau of China to analyze organic acid composition, content, and the expression levels of related regulated genes during fruit development. We found that the organic acid content in the variant was significantly lower than that in the ‘Golden Delicious’ apple. In both apples, quinic and malic acids were the predominant organic acids, while citric and tartaric acids were present in lower amounts. In this multidimensional regulatory study, we used transcriptome sequencing, cluster analysis, and weighted gene co-expression network analysis (WGCNA) to reveal that differentially expressed genes are enriched in multiple pathways affecting fruit acidity during apple development; malate dehydrogenase (MDH) affects the malic acid content of fruits of different varieties; and H+-ATPase (VHA) mainly regulates the content of vacuolar organic acids, which affects fruit acidity. Additionally, we performed qRT-PCR experiments to validate our results. This study provides molecular insights into the mechanisms by which low-acidity traits form in apples and offers a theoretical basis for regulating the flavor of fleshy fruits. Full article
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19 pages, 17437 KiB  
Article
Assessment of NUDT5 in Endometrial Carcinoma: Functional Insights, Prognostic and Therapeutic Implications
by Hongfei Yu, Lingling Zu, Yuqin Zang, Fei Teng, Tao Wang, Ming Wu, Yingmei Wang and Fengxia Xue
Biomedicines 2025, 13(5), 1136; https://doi.org/10.3390/biomedicines13051136 - 7 May 2025
Viewed by 190
Abstract
Background: Endometrial carcinoma (EC) is the most common gynecological malignancy, with increasing incidence contributing to a significant global health burden. Despite recent advancements, the molecular mechanisms underlying EC progression remain insufficiently understood, limiting the development of targeted therapies. This study aims to [...] Read more.
Background: Endometrial carcinoma (EC) is the most common gynecological malignancy, with increasing incidence contributing to a significant global health burden. Despite recent advancements, the molecular mechanisms underlying EC progression remain insufficiently understood, limiting the development of targeted therapies. This study aims to investigate the role of nucleoside diphosphate-linked moiety X motif 5 (NUDT5) in EC and evaluate its potential as a biomarker and therapeutic target. Methods: This study analyzed gene expression data from The Cancer Genome Atlas and performed tissue microarray validation to assess NUDT5 expression in EC samples. Immunohistochemistry was used to evaluate NUDT5 protein levels and their correlation with clinicopathological features. Functional assays, including cell proliferation, migration, invasion, and apoptosis analysis, were conducted to determine the oncogenic effects of NUDT5 in vitro. Weighted gene co-expression network analysis (WGCNA) and experimental validation were performed to explore the impact of NUDT5 on the PI3K-AKT signaling pathway, while tumor growth assays in xenograft models assessed the therapeutic potential of NUDT5 inhibition in vivo. Results: NUDT5 was significantly overexpressed in EC tissues and correlated with advanced histological grade and poor prognosis. Functional experiments demonstrated that NUDT5 promotes cell proliferation, migration, and invasion while inhibiting apoptosis. Mechanistically, NUDT5 activated the PI3K-AKT pathway, contributing to tumor progression. In vivo, NUDT5 knockdown suppressed tumor growth. Conclusions: These findings suggest that NUDT5 functions as an oncogene in EC, serving as a potential diagnostic and prognostic biomarker. Targeting NUDT5 may provide a novel therapeutic strategy for EC management. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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23 pages, 8247 KiB  
Article
The Key Role and Mechanism of Oxidative Stress in Hypertrophic Cardiomyopathy: A Systematic Exploration Based on Multi-Omics Analysis and Experimental Validation
by Sijie Zhang, Tianzhi Li, Shiyi Sun, Yujiao Jiang, Yuxin Sun and Yan Meng
Antioxidants 2025, 14(5), 557; https://doi.org/10.3390/antiox14050557 - 7 May 2025
Viewed by 220
Abstract
Hypertrophic cardiomyopathy (HCM), characterised by abnormal ventricular thickening, involves complex mechanisms including gene mutations, calcium dysregulation, mitochondrial dysfunction, and oxidative stress. Oxidative stress plays a pivotal role in the progression of HCM by mediating cardiomyocyte injury and remodelling. This study systematically analysed HCM [...] Read more.
Hypertrophic cardiomyopathy (HCM), characterised by abnormal ventricular thickening, involves complex mechanisms including gene mutations, calcium dysregulation, mitochondrial dysfunction, and oxidative stress. Oxidative stress plays a pivotal role in the progression of HCM by mediating cardiomyocyte injury and remodelling. This study systematically analysed HCM transcriptomic data using differential gene expression, weighted gene co-expression network analysis (WGCNA), and unsupervised consensus clustering to identify key genes and classify HCM subtypes. Four oxidative stress-related characteristic genes (DUSP1, CCND1, STAT3, and THBS1) were identified using LASSO regression, SVM-RFE, and Random Forest algorithms. Their functional significance was validated by immune infiltration analysis, drug prediction using the cMAP database, and molecular docking. Single-cell RNA sequencing revealed their cell-type-specific expression, and in vitro experiments confirmed their role in HCM. These findings provide insights into oxidative stress mechanisms and potential therapeutic targets for HCM. Full article
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20 pages, 5360 KiB  
Article
The Transcriptome Analysis Provides New Insights into Signaling for Bamboo Shoot Development of Sympodial Bamboo
by Shunkai Hu, Mengran Dong and Qirong Guo
Foods 2025, 14(9), 1647; https://doi.org/10.3390/foods14091647 - 7 May 2025
Viewed by 144
Abstract
Bamboo is a member of the Poaceae family and serves as an important economic resource with various applications, including reforestation, food production, and environmental conservation, due to its rapid growth and renewable nature. Among its various uses, bamboo shoots stand out for their [...] Read more.
Bamboo is a member of the Poaceae family and serves as an important economic resource with various applications, including reforestation, food production, and environmental conservation, due to its rapid growth and renewable nature. Among its various uses, bamboo shoots stand out for their tender texture and delicate flavor, making them a highly sought-after culinary delicacy in many cultures and a key ingredient in global food industries. Despite extensive research on the development of monopodial bamboos, studies focused on the developmental processes of sympodial bamboos, especially regarding their culinary potential, remain limited. This study conducted a comprehensive transcriptomic analysis of sympodial bamboo (Bambusa sp.) across six developmental stages (S1–S6) to uncover the molecular regulatory networks governing early bamboo shoot development. The results revealed that 1603 common differentially expressed genes (DEGs) across S1–S6 were enriched in multiple key pathways, with the most significant being plant hormone signaling, MAPK signaling, and Glycolysis/Gluconeogenesis pathways. Co-expression clustering analysis indicated that the Glycolysis/Gluconeogenesis pathway plays a crucial role during the later stages of bamboo shoot development (S5–S6), impacting its texture and flavor—two critical factors determining its culinary quality. Further Weighted Gene Co-expression Network Analysis (WGCNA) highlighted the significant role of the MAPK signaling pathway during early bamboo shoot development and identified key hub genes (MKK, MPK, MEKK) within this pathway, emphasizing their importance in cell division and hormonal coordination. This study provides valuable insights into the molecular mechanisms underlying the rapid growth and exceptional flavor of bamboo shoots and lays the foundation for the genetic improvement of bamboo as a sustainable and nutritious food source, enhancing its value as a premium food ingredient in the global market. Full article
(This article belongs to the Section Foodomics)
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12 pages, 5372 KiB  
Article
Identification of Hub Genes and Key Pathways Associated with Sepsis Progression Using Weighted Gene Co-Expression Network Analysis and Machine Learning
by Qinghui Sun, Hai-Li Zhang, Yichao Wang, Hao Xiu, Yufei Lu, Na He and Li Yin
Int. J. Mol. Sci. 2025, 26(9), 4433; https://doi.org/10.3390/ijms26094433 - 7 May 2025
Viewed by 146
Abstract
Sepsis is a life-threatening condition driven by dysregulated immune responses, resulting in organ dysfunction and high mortality rates. Identifying key genes and pathways involved in sepsis progression is crucial for improving diagnostic and therapeutic strategies. This study analyzed transcriptomic data from 49 samples [...] Read more.
Sepsis is a life-threatening condition driven by dysregulated immune responses, resulting in organ dysfunction and high mortality rates. Identifying key genes and pathways involved in sepsis progression is crucial for improving diagnostic and therapeutic strategies. This study analyzed transcriptomic data from 49 samples (37 septic patients across days 0, 1, and 8, and 12 healthy controls) using weighted gene co-expression network analysis (WGCNA) and multi-algorithm feature selection approaches. Differential expression analysis, pathway enrichment, and network analyses were employed to uncover potential biomarkers and molecular mechanisms. WGCNA identified modules such as MEbrown4 and MEblack, which strongly correlated with sepsis progression (r > 0.7, p < 0.01). Differential expression analysis highlighted up-regulated genes like CD177 and down-regulated genes like LOC440311. KEGG analysis revealed significant pathways including neuroactive ligand–receptor interaction, PI3K-Akt signaling, and MAPK signaling. Gene ontology analysis showed involvement in immune-related processes such as complement activation and antigen binding. Protein–protein interaction network analysis identified hub genes such as TNFSF10, IGLL5, BCL2L1, and SNCA. Feature selection methods (random forest, LASSO regression, SVM-RFE) consistently identified top predictors like TMCC2, TNFSF10, and PLVAP. Receiver operating characteristic (ROC) analysis demonstrated high predictive accuracy for sepsis progression, with AUC values of 0.973 (TMCC2), 0.969 (TNFSF10), and 0.897 (PLVAP). Correlation analysis linked key genes such as TNFSF10, GUCD1, and PLVAP to pathways involved in immune response, cell death, and inflammation. This integrative transcriptomic analysis identifies critical gene modules, pathways, and biomarkers associated with sepsis progression. Key genes like TNFSF10, TMCC2, and PLVAP genes show strong diagnostic potential, providing novel insights into sepsis pathogenesis and offering promising targets for future therapeutic interventions. Among these, TNFSF10 and PLVAP are known to encode secreted proteins, suggesting their potential as circulating biomarkers. This enhances their translational relevance in clinical diagnostics. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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22 pages, 6697 KiB  
Article
Integrated Multi-Tissue Lipidomics and Transcriptomics Reveal Differences in Lipid Composition Between Mashen and Duroc × (Landrace × Yorkshire) Pigs
by Mingyue Shi, Wenxia Li, Shuai Yang, Qipin Lv, Jingxian Yang, Di Sun, Guanqing Yang, Yan Zhao, Wanfeng Zhang, Meng Li, Yang Yang, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li and Guoqing Cao
Animals 2025, 15(9), 1280; https://doi.org/10.3390/ani15091280 - 30 Apr 2025
Viewed by 321
Abstract
Chinese native pig breeds exhibit unique advantages over Western pig breeds, but the specific lipid metabolism mechanisms remain unclear. The phenotypic characteristics of Mashen (MS) pigs and Duroc × (Landrace × Yorkshire) (DLY) pigs are studied. The results show that MS pigs exhibit [...] Read more.
Chinese native pig breeds exhibit unique advantages over Western pig breeds, but the specific lipid metabolism mechanisms remain unclear. The phenotypic characteristics of Mashen (MS) pigs and Duroc × (Landrace × Yorkshire) (DLY) pigs are studied. The results show that MS pigs exhibit higher intramuscular fat (IMF) content. The area of adipocytes of MS pigs is significantly greater than that in DLY pigs (p < 0.01). Lipidomics analysis reveals distinct profiles in the upper layer of backfat (ULB), leaf lard (LL), greater omentum (GOM), and IMF, with MS pigs showing higher polyunsaturated fatty acids (PUFAs) in ULB, LL, and GOM. Key differential lipids identified in the two pig breeds include the following triglycerides (TGs) and phosphatidylcholines (PC): TG(16:1_18:1_18:3), TG(18:1_18:2_18:3), TG(18:3_18:2_18:2), PC(18:0_18:1), and PC(18:0_18:2). Weighted gene co-expression network analysis (WGCNA) reveals lipid molecules associated with serum biochemical indices. Transcriptomics analysis highlights 1944 differentially expressed genes between the MS-ULB and DLY-ULB. Notably, multiple genes from the cytochrome P450 family (CYP2E1, CYP4A24, CYP2J2), along with PLA2G2D, PLA2G4A, and multiple PCs, are associated with the metabolism of arachidonic acids and linoleic acids. PLA2G2D and PLA2G4A are also involved in the metabolism of α-linolenic acids. This comprehensive analysis provides essential information for breeding strategies and meat quality improvement. Full article
(This article belongs to the Section Pigs)
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19 pages, 4883 KiB  
Article
Transcriptomic Profiling of Heat-Treated Oriental Lily Reveals LhERF109 as a Positive Regulator of Anthocyanin Accumulation
by Mei Zhou, Lijia Zeng, Fan Li, Chunlian Jin, Jungang Zhu, Xue Yong, Mengxi Wu, Beibei Jiang, Yin Jia, Huijuan Yuan, Jihua Wang and Yuanzhi Pan
Agronomy 2025, 15(5), 1071; https://doi.org/10.3390/agronomy15051071 - 28 Apr 2025
Viewed by 253
Abstract
Pink-flowered Oriental lily cultivars exhibit significant color fading under high temperatures, but the underlying regulatory mechanisms remain unclear. We subjected ‘Souvenir’ Oriental lily plants to temperature treatments (20 °C and 35 °C) and performed transcriptome sequencing and weighted gene co-expression network analysis (WGCNA). [...] Read more.
Pink-flowered Oriental lily cultivars exhibit significant color fading under high temperatures, but the underlying regulatory mechanisms remain unclear. We subjected ‘Souvenir’ Oriental lily plants to temperature treatments (20 °C and 35 °C) and performed transcriptome sequencing and weighted gene co-expression network analysis (WGCNA). The high temperature (35 °C) significantly reduced the anthocyanin content in tepals. The transcriptome analysis identified 8354 differentially expressed genes, with the GO and KEGG analyses revealing a dynamic transition from early stress responses to metabolic adaptation. The WGCNA revealed a module strongly correlated with the anthocyanin content, from which we constructed a gene co-expression network using known anthocyanin-related genes, including the key transcription factor LhMYB12 and structural genes involved in the anthocyanin biosynthetic pathway (LhANS, LhDFR, LhUGT78, and LhF3′H). Through this comprehensive network analysis, we successfully identified and screened LhERF109 as a promising regulatory candidate. The transient overexpression of LhERF109 was found to enhance anthocyanin accumulation and upregulate biosynthetic genes including LhMYB12, while silencing LhERF109 expression produced the opposite effects. These findings identify LhERF109 as a positive regulator of anthocyanin biosynthesis under high temperatures, providing new targets for breeding heat-tolerant lilies with stable flower coloration. Full article
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27 pages, 4786 KiB  
Article
Transcriptomic Regulatory Mechanisms of Isoflavone Biosynthesis in Trifolium pratense
by Kefan Cao, Sijing Wang, Huimin Zhang, Yiming Ma, Qian Wu, Fan Huang and Mingjiu Wang
Agronomy 2025, 15(5), 1061; https://doi.org/10.3390/agronomy15051061 - 27 Apr 2025
Viewed by 175
Abstract
Isoflavones are important secondary metabolites in leguminous plants with significant physiological functions and economic value. However, the genetic variation, transcriptional regulation, and metabolic pathways governing isoflavone biosynthesis in Trifolium pratense remain largely unexplored. In this study, we systematically analyzed 500 accessions of T. [...] Read more.
Isoflavones are important secondary metabolites in leguminous plants with significant physiological functions and economic value. However, the genetic variation, transcriptional regulation, and metabolic pathways governing isoflavone biosynthesis in Trifolium pratense remain largely unexplored. In this study, we systematically analyzed 500 accessions of T. pratense for isoflavone content and performed RNA-seq-based transcriptomic profiling to investigate the molecular mechanisms underlying isoflavone biosynthesis. Cluster analysis revealed significant genetic variation, with distinct transcriptional profiles between high- (H1, H2, H3) and low-isoflavone (L1, L2, L3) groups. GO and KEGG pathway enrichment analyses identified key metabolic pathways, including phenylpropanoid metabolism, flavonoid biosynthesis, carbohydrate metabolism, and hormone signaling, which play crucial roles in isoflavone regulation. Weighted gene co-expression network analysis (WGCNA) identified three key gene modules—MEblue, MEturquoise, and MEyellow—strongly correlated with isoflavone content. The MEturquoise and MEyellow modules were upregulated in high-isoflavone groups and were enriched in phenylpropanoid biosynthesis, lipid metabolism, and transcriptional regulation, suggesting that these pathways actively promote isoflavone accumulation. Conversely, the MEblue module, highly expressed in low-isoflavone groups, was enriched in sugar metabolism and MAPK signaling, indicating a potential metabolic flux shift away from secondary metabolism. Moreover, key rate-limiting enzymes (PAL, C4H, 4CL, CHS, and IFS) exhibited higher expression in high-isoflavone groups, highlighting their importance in precursor supply and enzymatic catalysis. Additionally, transcription factors such as MYB, WRKY, and NAC were identified as potential regulators of isoflavone biosynthesis, indicating a complex interplay between hormonal, circadian, and environmental signals. This study provides a comprehensive molecular framework for understanding isoflavone biosynthesis in T. pratense and identifies key regulatory genes and metabolic pathways that could be targeted for genetic improvement, metabolic engineering, and molecular breeding. The findings offer valuable insights into enhancing isoflavone production in legumes for agricultural, nutritional, and pharmaceutical applications. Full article
(This article belongs to the Section Plant-Crop Biology and Biochemistry)
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16 pages, 3504 KiB  
Article
Comparative Proteome and Weighted Gene Co-Expression Network Analyses Uncover the Mechanism of Wheat Grain Protein Accumulation in Response to Nitrogen Fertilizer Application
by Beiming Xu, Yuku Jia, Jianchao Feng, Yang Yang, Geng Ma, Yanfei Zhang, Yingxin Xie and Dongyun Ma
Foods 2025, 14(9), 1481; https://doi.org/10.3390/foods14091481 - 24 Apr 2025
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Abstract
This study uses proteomic technology to identify differentially expressed proteins (DEPs) under varying nitrogen fertilizer levels. Additionally, it utilizes weighted gene co-expression network analysis (WGCNA) based on expression data of DEP-coding genes to explore the mechanism by which nitrogen promotes grain protein accumulation. [...] Read more.
This study uses proteomic technology to identify differentially expressed proteins (DEPs) under varying nitrogen fertilizer levels. Additionally, it utilizes weighted gene co-expression network analysis (WGCNA) based on expression data of DEP-coding genes to explore the mechanism by which nitrogen promotes grain protein accumulation. The results indicate that high-nitrogen treatment leads to an increased grain protein content, wet gluten content, stability time, and energy area. In addition, the β-sheet content of the protein secondary structure increased, while the irregular curl content decreased. A total of 285 DEPs were identified under different nitrogen levels, with 172 upregulated proteins in grains under high-nitrogen treatment including storage proteins (8.14%) and proteins involved in nitrogen metabolism (8.72%), defense/stress (11.04%), regulation (26.16%), and transport (5.23%). This suggests that both storage proteins and certain metabolic proteins contribute to dough network formation. WGCNA revealed a strong correlation between the blue module and grain samples, and Gene Ontology analysis indicated that most genes were enriched in response to abscisic acid (ABA) in the “biological process” category. Furthermore, 18 core genes were identified, with most containing ABA response elements, light response elements, and motifs related to storage protein regulation in their promoter regions. Expression analysis of 10 genes and their predicted transcription factors during the grain-filling stage demonstrated higher expression levels under high-nitrogen conditions. This study provides valuable insights into the promotion of grain protein accumulation and dough quality by nitrogen fertilizer application. Full article
(This article belongs to the Section Foodomics)
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