Permanent crop cover as a strategy for drought-resistant viticulture: insights on how rhizosphere metagenomics influences leaf-level -omics for an enhanced overall plant response by Iván Jáuregui, María Ancín, José M. García-Mina, José M. García-Mina, Angel M. Zamarreño, Angel M. Zamarreño, Ariadna Iglesias-Sanchez, Ariadna Iglesias-Sanchez, Igor Florez-Sarasa, Igor Florez-Sarasa, Iker Aranjuelo

“…Through comprehensive examinations of gas exchange, isotopic analysis, metabolomics, transcriptomics, and soil metagenomics, this study clarifies the relationships among irrigation methodologies, photosynthesis, and soil health, ultimately aiding in the fortification of agricultural resilience in the face of climate change. …”
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The involvement of PsTCP genes in hormone-mediated process of bud dormancy release in tree peony (Paeonia suffruticosa) by Qianqian Wang, Bole Li, Zefeng Qiu, Jiayi Ying, Xuyichen Jin, Zeyun Lu, Junli Zhang, Xia Chen, Xiangtao Zhu

“…Furthermore, the endogenous hormone levels provided evidence for the substantial impact of exogenous GA3 on dormancy release, highlighting its potential involvement in the chilling-independent pathway of dormancy release. Transcriptome sequencing and analysis of expression profiles were conducted to identify the crucial genes implicated in the dormancy release mechanism of tree peony. …”
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Screening and comparison of in vitro-induced resistant and clinically resistant Stenotrophomonas maltophilia strains for eravacycline resistance-related genes by Jie Wu, Jiarong Song, Junchang Cui

“…Transcriptome analysis revealed consistent upregulation of efflux pump genes (smrA, smeD, smeE, smeF) across all induced strains. …”
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Auxin Controls Root Gravitropic Response by Affecting Starch Granule Accumulation and Cell Wall Modification in Tomato by Huabin Liu, Yue Wu, Jiahui Cai, Lele Xu, Cheng Zhou, Chengliang Wang

“…Transcriptome analysis revealed that many (2770) differentially expressed genes (DEGs) were identified in roots following 36 h of gravity stimulation. …”
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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

“…Through Weighted Gene Co-expression Network Analysis (WGCNA) analysis, we identified two modules MEblueviolet and MEgreenyellow related to terpenoids (floral scents) and carotenoids (floral colors) biosynthesis. …”
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Genome-Wide Characterization of the <i>SnRK</i> Gene Family in <i>Taxus</i> and Homologous Validation of <i>TaSnRK1.2</i> as a Central Regulator in Stress-Responsive Transcriptiona... by Pengjun Lu, Jianqiu Ji, Fangjuan Fan, Tao Liu, Zhenting Shi, Wentao Li, Chongbo Sun

“…Specifically, we identified <i>SnRK</i> genes through genomic analysis and assessed tissue-specific expression via transcriptomics, while regulatory networks were deciphered using WGCNA. …”
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Response mechanism of ethanol-tolerant Saccharomyces cerevisiae strain ES-42 to increased ethanol during continuous ethanol fermentation by Xue-Xue Ji, Quan Zhang, Bai-Xue Yang, Qing-Ran Song, Zhao-Yong Sun, Cai-Yun Xie, Yue-Qin Tang

“…Cells were collected at different ethanol concentrations (from 60 g/L to 100 g/L) for comparative transcriptomic analysis. Results During continuous fermentation, as ethanol concentration increased, the expression of genes associated with cytoplasmic ribosomes, translation, and fatty acid biosynthesis progressively declined, while the expression of genes related to heat shock proteins (HSPs) and ubiquitin-mediated protein degradation gradually increased. …”
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Environmental adaptation and reproductive mechanisms of Codium fragile subsp. fragile in the Bohai Bay by Jingjing Zi, Zhiying Wang, Lanping Ding

“…Transcriptomic analysis revealed significant temperature-dependent effects (20°C and 25°C) on both growth and reproduction, with 2668 differentially expressed genes (DEGs), of which 1663 were upregulated. …”
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Regulatory mechanism of Haa1p and Hap4p in Saccharomyces cerevisiae to mixed acetic acid and formic acid when fermenting mixed glucose and xylose by Xin-Yu Xiao, Bo Li, Zi-Yuan Xia, Quan Zhang, Cai-Yun Xie, Yue-Qin Tang

“…This study aimed to further elucidate their regulatory roles in conferring tolerance to this combined stress condition. Comparative transcriptomic analysis was conducted using the engineered strains s6H3 (HAA1-overexpressing) and s6P5 (HAP4-overexpressing), in comparison with the original strain s6. …”
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Emission and Transcriptional Regulation of Aroma Variation in <i>Oncidium</i> Twinkle ‘Red Fantasy’ Under Diel Rhythm by Yan Chen, Shengyuan Zhong, Lan Kong, Ronghui Fan, Yan Xu, Yiquan Chen, Huaiqin Zhong

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Dysregulation of innate and adaptive lymphoid immunity may have implications for symptom attribution and predict responses to targeted therapies in neuropsychiatric systemic lupus... by Julius Lindblom, Guillermo Barturen, Lorenzo Beretta, Daniel Toro-Domínguez, Elena Carnero-Montoro, Maria Orietta Borghi, Jessica Castillo, Ellen Iacobaeus, Yvonne Enman, Chandra Mohan, Marta E. Alarcón-Riquelme, Dionysis Nikolopoulos, Ioannis Parodis, Jacques-Olivier Pers, Alain Saraux, Valérie Devauchelle-Pensec, Sandrine Jousse-Joulin, Bernard Lauwerys, Julie Ducreux, Anne-Lise Maudoux, Ana Tavares, Isabel Almeida, Miguel Angel Gonzalez-Gay Mantecón, Ricardo Blanco Alonso, Alfonso Corrales Martínez, Ignasi Rodríguez-Pintó, Gerard Espinosa, Rik Lories, Nicolas Hunzelmann, Doreen Belz, Niklas Baerlecken, Michael Zauner, Michaela Lehner, Eduardo Collantes, Ma Angeles Aguirre-Zamorano, Alejandro Escudero-Contreras, Ma Carmen Castro-Villegas, Norberto Ortego, María Concepción Fernández Roldán, Enrique Raya, Inmaculada Jiménez Moleón, Enrique de Ramon, Isabel Díaz Quintero, Pier Luigi Meroni, Tommaso Schioppo, Carolina Artusi, Carlo Chizzolini, Aleksandra Zuber, Donatienne Wynar, Attila Balog, Magdolna Deák, Márta Bocskai, Sonja Dulic, Gabriella Kádár, Falk Hiepe, Silvia Thiel, Manuel Rodriguez Maresca, Antonio López-Berrio, Rocío Aguilar-Quesada, Héctor Navarro-Linares

“…Lastly, we performed regulatory network and druggability analysis. Results: Unsupervised weighted gene co-expression network analysis (WGCNA) revealed 23 dysregulated gene modules and two subgroups of active CNS lupus. …”
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Modulation of gut microbiota by Gardeniae Fructus oil exerts TLR4/NF-κB/NLRP3 pathway-mediated antidepressant effects based on transcriptomics and fecal transplantation by Man Han, Man Han, Man Han, Yujing Zhou, Yujing Zhou, Yujing Zhou, Xinyu Gao, Xinyu Gao, Xinyu Gao, Xixi Cheng, Xixi Cheng, Xixi Cheng, Ling Deng, Ling Deng, Ling Deng, Shilin Ji, Shilin Ji, Shilin Ji, Zhengheng Li, Zhengheng Li, Zhengheng Li, Yu Cai, Yu Cai, Yu Cai, Chunchao Yan, Chunchao Yan, Chunchao Yan, Yunzhong Chen, Yunzhong Chen, Yunzhong Chen

“…The signaling pathways regulating the antidepressant properties of OGF were obtained by transcriptome sequencing analysis and validated at the protein level.ResultsCompared with the CON group, mice in the CUMS group showed significant depressive-like behavior, pathological damage to the hippocampus and colon tissues, significant decrease in levels of 5-HT, DA, and BDNF in the hippocampus, significant increase in levels of IL-1β, IL-6, TNF-α, DAO, and LPS in serum, significant decrease in colonic tight junction protein expression, and significant increase in protein expression of TLR4, p-NF-κB, NLRP3, ASC, and IL-1β in the hippocampus (P &lt; 0.01); Compared with the CUMS group, the FMT group could effectively improve the above situation (P &lt; 0.05, P &lt; 0.01), whose therapeutic effect was second only to the OGF group (P &lt; 0.01), while ABX + OGF group did not show obvious therapeutic effect.ConclusionOGF might exert antidepressant effects by modulating gut microbiota and mediating the hippocampal TLR4/NF-κB/NLRP3 pathway.…”
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Diurnal rhythms in durum wheat triggered by Rhopalosiphum padi (bird cherry-oat aphid) by Yoshiahu Goldstein, Jinlong Han, Daniel Kunk, Albert Batushansky, Vamsi Nalam, Vered Tzin

“…Under control conditions, 15,366 out of the 66,559 genes in the tetraploid wheat cultivar Svevo, representing approximately 25% of the transcriptome, exhibited diurnal rhythmicity. Upon aphid infestation, 5,682 genes lost their rhythmicity, while 5,203 genes began to exhibit diurnal rhythmicity. …”
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Preharvest Application of Exogenous 2,4-Epibrassinolide and Melatonin Enhances the Maturity and Flue-Cured Quality of Tobacco Leaves by Kesu Wei, Jiayi Tang, Lei Yang, Shaopeng Chen, Zhijun Cheng, Yijun Yang, Chen Xu, Shengjiang Wu, Yuhang Zhao, Hongmei Di, Ling Li, Dongyang Sun, Jianwei Li, Bo Sun

“…The levels of conventional chemical components were improved, enhancing the overall coordination of the tobacco. Transcriptome analysis revealed that EBR treatment down-regulated the chlorophyll biosynthetic genes <i>hemA</i>, <i>MgPEC</i>, and <i>ChlD</i>, while up-regulating the chlorophyll degradation genes <i>CHL2</i>, <i>SGR</i>, and <i>PAOs</i>. …”
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Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions by Konstantina Athanasopoulou, Vasiliki-Ioanna Michalopoulou, Andreas Scorilas, Panagiotis G. Adamopoulos

“…AI-driven tools, including machine learning and deep learning, enhance every aspect of NGS workflows—from experimental design and wet-lab automation to bioinformatics analysis of the generated raw data. Key applications of AI integration in NGS include variant calling, epigenomic profiling, transcriptomics, and single-cell sequencing, where AI models such as CNNs, RNNs, and hybrid architectures outperform traditional methods. …”
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High-throughput sequencing unravels placental vascular dysfunction and oxidative stress as mechanistic drivers of advanced maternal age-associated pregnancy by Xin Sun, Yao Chen, Feifei Hu, Yumeng Qiao, He Wu, Yao Su, Yue Hu, Jie Wu, Jie Wu, Mingli Huang

“…IntroductionWomen with advanced maternal age (AMA) face a higher risk of pregnancy complications including preeclampsia, fetal growth restriction, and preterm birth. While placental dysfunction is implicated, the underlying mechanisms remain unclear. …”
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Mapping the molecular signature of ABA-regulated gene expression in germinating barley embryos by Ewa Sybilska, Bahareh Sadat Haddadi, Luis A. J. Mur, Manfred Beckmann, Szymon Hryhorowicz, Joanna Suszynska-Zajczyk, Monika Knaur, Andrzej Pławski, Agata Daszkowska-Golec

“…Results Transcriptomic analysis indicated that ABA acts primarily as a germination repressor. …”
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Knowledge of the genetics of human pain gained over the last decade from next-generation sequencing by Dario Kringel, Jörn Lötsch

“…This approach allows the analysis of cellular changes during the development of chronic pain. …”
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Sex-specific differences in preclinical models of advanced chronic liver disease and portal hypertension by Peio Aristu-Zabalza, María Andrés-Rozas, Zoe Boyer-Díaz, David P. Al-Adra, Douglas Maya-Miles, Sergi Guixé-Muntet, Anabel Fernández-Iglesias, Jordi Gracia-Sancho

“…In the BDL model, females had more fenestrae and porosity, and less fibrosis. Transcriptomic analysis revealed that TAA males had dysregulated metabolic pathways, while females had deregulated genes in hormone signaling. …”
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Investigating the Mechanisms Underlying Citral-Induced Oxidative Stress and Its Contribution to Antifungal Efficacy on <i>Magnaporthe oryzae</i> Through a Multi-Omics Approach by Yonghui Huang, Ruoruo Wang, Yumei Tan, Yongxiang Liu, Xiyi Ren, Congtao Guo, Rongyu Li, Ming Li

“…Furthermore, RNA-seq analysis and metabolomics analysis identified a total of 466 differentially expression genes (DEGs) and 32 differential metabolites (DAMs) after the mycelia were treated with citral. …”
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