Transcriptome and Metabolome Analyses of <i>Taxus chinensis</i> var. <i>mairei</i> Tissues Provide New Insights into the Regulation of Paclitaxel Biosynthesis by Luyuan Jiang, Yanyan Li, Xiaoyang Jiang, Fenjuan Shao, Wenli Wu, Fan Xu, Iain Wilson, Angela Hoffman, Yanfang Yang, Deyou Qiu

“…In this study, we conducted integrated transcriptomic and metabolomic analyses of the root, leaf, shoot, bark, and wood of <i>Taxus chinensis</i> var. …”
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Comparative Physiological and Transcriptomics Profiling Provides Integrated Insight into Melatonin Mediated Salt and Copper Stress Tolerance in <i>Selenicereus undatus</i> L. by Darya Khan, Xin Yang, Gong He, Raja Asad Ali Khan, Babar Usman, Liu Hui, Aamir Ali Khokhar, Qamar U Zaman, Hua-Feng Wang

“…Antioxidant activities were also modulated by stress. Transcriptomic analysis revealed 21 differentially expressed genes (DEGs) common across stress treatments and 13 DEGs specific to combined melatonin with stress treatments involved in stress signaling, secondary metabolite biosynthesis, and photosynthesis. …”
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Transcriptomics and non-targeted metabolomics provide mechanistic insights into the improvement of the growth performance and meat quality of lambs supplemented with fermented Lycium barbarum residues by Jiale Liao, Wencan Ke, Bing Wang, Min Du, Qiang Lu, Yajun Zhang, Guijie Zhang

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Beneficial mutualistic fungus Suillus luteus provided excellent buffering insurance in Scots pine defense responses under pathogen challenge at transcriptome level by Zilan Wen, Minna J. Manninen, Fred O. Asiegbu

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Correction: Comprehensive analysis of transcriptomics and metabolomics provides insights into the mechanism by plant growth regulators affect the quality of jujube (Ziziphus jujuba Mill.) fruit. by PLOS One Staff

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The chromosome-level genome of Hemerocallis middendorffii provides new insights into the floral scents and color biosynthesis in Chinese native daylily by Meiyu Sun, Baocai Han, Jianhua Xiao, Haiyan Yu, Yinli Jia, Shuhai Yuan, Juan Yao, Quan Xing, Dongqi Wu, Guofeng Sun, Jinzheng Zhang

“…We employed a combination of genomic, transcriptomic, and metabolomic approaches to investigate mechanisms behind the floral scent and color biosynthesis in daylily. …”
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A comprehensive analysis of the defense responses of Odontotermes formosanus (Shiraki) provides insights into the changes during Serratia marcescens infection by Zhiqiang Wang, Mingyu Wang, Yujingyun Zhou, Kai Feng, Fang Tang

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Multi-Omics Analysis Provides Insights into a Mosaic-Leaf Phenotype of Astaxanthin-Producing Tobacco by Jialin Wang, Zaifeng Du, Xiaoyang Lin, Peng Li, Shihao Sun, Changqing Yang, Yong Chen, Zhongfeng Zhang, Xue Yin, Ning Fang

“…Then, metabolomics, proteomics, and small RNA transcriptomics were employed to analyze the uneven distribution of astaxanthin-producing regions in tobacco leaves. …”
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Comparative transcriptomic analysis and genome-wide identification provide insights into the potential role of fungal-responsive MAPK cascade genes in tanshinone accumulation in Salvia miltiorrohiza by Ann Abozeid, Ann Abozeid, Xinru Du, Lan Zhang, Furui Yang, Jianxiong Wu, Lin Zhang, Qi Cui, Zongqi Yang, Dongfeng Yang, Dongfeng Yang

“…The presence of defense-related cis-acting elements in the promoter regions of SmMPK4, SmMPKK5, SmMPKKK6, SmMPKKK11, and SmMPKKK20 further supports their involvement in fungal elicitor-mediated tanshinone accumulation. This study provides critical insights into the regulatory roles of SmMAPK genes in tanshinone accumulation in S. miltiorrhiza in response to fungal elicitors. …”
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Comprehensive transcriptome analysis provides molecular insights into the heterosis-associated drought tolerance and reveals ZmbHLH137 that promotes drought tolerance in maize seedlings by Liru Cao, Dongling Zhang, Abbas Muhammad Fahim, Huafeng Liu, Zhe Zhang, Desheng Hu, Feiyu Ye, Chenchen Ma, Salah Fatouh Abou-Elwaf, Nora M. Al Aboud, Yinghui Song, Shulei Guo, Qianjin Zhang, Xin Zhang, Xiaomin Lu

“…These results indicate that ZmbHLH137 positively regulates drought tolerance in maize at the seedling stage by regulating antioxidant enzyme activity. These findings provide novel insights into heterosis regulation in maize seedlings. …”
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Molecular profiling of bladder cancer xenografts defines relevant molecular subtypes and provides a resource for biomarker discovery. by Sharada Mokkapati, Ganiraju Manyam, Alexis R. Steinmetz, Côme Tholomier, Alberto Martini, Woonyoung Choi, Bogdon Czerniak, Byron H Lee, Colin P Dinney, David J McConkey

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Comparative Genomic and Transcriptomic Analysis Provides New Insights into the Aflatoxin B₁ Biodegradability by <i>Kocuria rosea</i> from Deep Sea by Jingying Wang, Jun Nan

“…In addition, this study revealed 1421 differentially expressed genes and 752 upregulated genes between the aflatoxin group and the control group through transcriptome analysis and conducted functional annotation and analysis of functional enrichment. …”
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Histological and transcriptome analysis provides new insights into the hematopoietic and immune functions of head kidney, trunk kidney and spleen of adult large yellow croaker, Larimichthys crocea by Aihua Zhong, Yingbin Wang, Haiqi Zhang, Xiaojun Yan, Shuo Jia

“…The large yellow croaker (Larimichthys crocea), a vital marine-cultured fish in Asia, lacks bone marrow and lymph nodes, relying instead on the head kidney (HK), trunk kidney (TK), and spleen for hematopoiesis and immune functions. This study provides a comprehensive histological and transcriptomic analysis of these organs in adult large yellow croaker, revealing their normal physiological roles in hematopoiesis and immunity. …”
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Transcriptomic Analysis Provides Insights into the Energetic Metabolism and Immune Responses in <i>Litopenaeus vannamei</i> Challenged by <i>Photobacterium damselae</i> subsp.... by Libao Wang, Qiuwen Xu, Zhijun Yu, Zhenxin Hu, Hui Li, Wenjun Shi, Xihe Wan

“…To explore the molecular mechanisms of the <i>Litopenaeus vannamei</i> response to infection by <i>Photobacterium damselae</i>, reveal its immune response and energetic metabolic effect, and provide a valuable genetic data source for the scientific prevention and control of <i>Vibrio</i> infection, transcriptomic analysis, RT-qPCR, and physiological and biochemical tests were conducted. …”
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Telomere-to-Telomere Assembly of the <i>Cordyceps militaris</i> CH1 Genome and Integrated Transcriptomic and Metabolomic Analyses Provide New Insights into Cordycepin Biosynthesis Under Light Stress by Yang Yang, Jingjing Huang, Gangqiang Dong, Xuebo Hu

“…This comprehensive analysis not only provides new insights into the genomics, metabolomics, and functional gene research of <i>C. militaris</i> CH1 but also offers a potential biological foundation for understanding the synthesis mechanisms of cordycepin and its efficient production.…”
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The dawn of spatiotemporal transcriptomics by Siying Wang, Shichao Lin, Chaoyong Yang

“…We further provide future outlooks for the rapid development of spatiotemporal transcriptomics technologies. …”
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The impact of anesthetics on the transcriptome by Anna Pilarz, Joanna Brzoza, Marcin Tomsia

“…The aim of the study is to review the latest literature on the impact of anesthetics on the transcriptome and the human body. A wide range of variations arising from the use of anesthetics has been presented, along with their effects that may extend beyond the perioperative period. …”
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Multi-Omics Analysis Provides New Insights into the Interplay Between Gut Microbiota, Fatty Acid Metabolism, and Immune Response in Cultured and Wild <i>Coilia nasus</i> from the Y... by Chang Yang, Kai Liu, Yanmin Deng, Qianhui Wang, Shiqian Cao, Qunlan Zhou

“…These differences, likely due to gut microbiota variations, provide insights for <i>C. nasus</i> nutritional studies.…”
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Transcriptome analysis of wild olive (Olea Europaea L. subsp. europaea var. sylvestris) clone AC18 provides insight into the role of lignin as a constitutive defense mechanism underlying resistance to Verticillium wilt by Beatriz Mascuñano, Jerónimo Coto-Elena, Víctor M. Guerrero-Sánchez, Candelas Paniagua, Rosario Blanco-Portales, José L. Caballero, José L. Trapero-Casas, Rafael M. Jiménez-Díaz, Fernando Pliego-Alfaro, José A. Mercado, Juan Muñoz-Blanco, Francisco J. Molina-Hidalgo

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Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma by Wanchen Cao, Kai Gao, Yi Zhao

“…This study conducted in-depth research and analysis on these potential biomarkers and key cells, providing new research foundations and insights for future basic experimental research and the diagnosis and treatment of PTC in clinical settings.…”
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