Full-Length Transcriptome Analysis of <i>Sesbania cannabina</i> Stem Response to Waterlogging Stress by Tingting He, Guoli Sun, Sunan He, Zhenhua Zhang, Jing Dong, Xiaomei Zhu, Jinying Dai, Kai Wang, Jincheng Xing

“…The assembly and annotation of full-length transcriptome data of <i>Sesbania</i> provided reliable and accurate genomic information for the exploration of key genes and the study of molecular mechanisms in stem response to waterlogging stress.…”
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Dynamic transcriptomic responses to soybean cyst nematode infection in soybean genotypes with contrasting resistance profiles by Nour Nissan, Nour Nissan, Nathalie Puchacz, Julia C. Hooker, Julia C. Hooker, Dave T. Ste-Croix, Gerardo Zapata, François Lefebvre, Martin Charette, Ashkan Golshani, Elroy Cober, Benjamin Mimee, Bahram Samanfar, Bahram Samanfar

“…This study explores the diversity of defense strategies and provides valuable insight into novel genetic origins of SCN resistance as we navigate the landscape of evolving SCN parasitism.…”
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Decoding pilocarpine biosynthesis and its roles in Pilocarpus microphyllus through a comparative transcriptomics approach by Mariane Brom Sobreiro, Giordano Bruno Soares-Souza, Leandro Magalhães, Débora de Morais Cordeiro, Michele Molina, Santelmo Vasconcelos, Yan Nunes Dias, Renato R. Moreira-Oliveira, Markus Gastauer, Silvio Ramos, Guilherme Oliveira, Cecílio Frois Caldeira, Amanda F. Vidal

“…This study presents the first comparative transcriptomic analysis in jaborandi by investigating gene expression across four different tissues (leaflets, rachis, root, and stem) and exploring potential pathways and functions involved in pilocarpine biosynthesis. …”
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Single‐Cell Transcriptome Reveals Aquaporin‐Mediated Carbon Nanosol‐Induced Growth Promotion of Plants by Lingtong Cheng, Zechao Qu, Qiansi Chen, Lin Wang, Huan Su, Jiemeng Tao, Peng Lu, Taibo Liang, Jianfeng Zhang, Peijian Cao, Jingjing Jin

“…Overall, these results provide new insights into the mechanism by which CNS promotes plant growth at the single‐cell level.…”
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Transcriptome Analysis Unveils the Molecular Mechanisms of Ethylene-Induced Ready-to-Eat Kiwifruit-Picking Ripening by Jiayi Zhang, Shangqiao Cao, Na Li, Hongbo Li, Zhenbin Liu, Dan Xu, Haizhen Mo

“…The primary objective of the present study was to comprehensively analyze the transcriptome to investigate the ripening mechanism of ethylene-induced ready-to-eat kiwifruit. …”
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HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets by Franco Liberati, Taiel Maximiliano Pose Marino, Paolo Bottoni, Daniele Canestrelli, Tiziana Castrignanò

“…The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.…”
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Integrated transcriptomic and metabolomic analyses reveal the molecular mechanism of flower color differentiation in Orychophragmus violaceus by Yubin Shi, Zixuan Wang, Zhuangzhuang Yan, Jianfeng Liu, Jun Zhang, Guixia Liu

“…By integrating metabolomic and transcriptomic data, OvANS, which encodes anthocyanidin synthase, was significantly upregulated in purple flowers. …”
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Single-cell transcriptomics reveals metabolic remodeling and functional specialization in the immune microenvironment of bone tumors by Jun Chen, Na Cui, Shao-Hui He, Chun-Yan Xia, Wei-Qing Li

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Host Immune Response to Clinical Hypervirulent Klebsiella pneumoniae Pulmonary Infections via Transcriptome Analysis by Langhuan Lei, Xiaoli Zhang, Rui Yang, Haiming Jing, Yue Yuan, Zhifu Chen, Qiang Gou, Zhuo Zhao, Jinyong Zhang, Xingyong Wang

“…Herein, we report a transcriptome analysis of the lungs from a mouse pneumonia model infected with a newly isolated K. pneumoniae clinical strain YBQ. …”
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Hongyuyin attenuates intestinal fibrosis in ulcerative colitis in mice revealed by transcriptomic and network pharmacology analyses by Qin Qin, Qingjun Dong, Yan Pan, Chen Wang, Jingen Lu

“…Clinical symptoms, colonic pathological damage, inflammation, and fibrosis were monitored across all groups. Both transcriptomic analysis and network pharmacology (NP) techniques were utilized to elucidate the mechanistic insights. …”
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Soil-Mulching Treatment Enhances the Content of Stilbene in Grape Berries: A Transcriptomic and Metabolomic Analysis by Bo Wang, Weimin Wu, Zhuangwei Wang, Zhenxiao Chen, Xicheng Wang

“…In this study, variations in the gene sets and metabolites of grape berries after mulching (rice straw + felt + plastic film) using transcriptome and metagenomic sequencing were investigated. …”
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Transcriptomic and Metabolomic Insights into Key Genes Involved in Kinsenoside Biosynthesis in <i>Anoectochilus roxburghii</i> by Peiyu Wang, Peipei Yan, Zunwen Li, Jinlan Jiang, Yuling Lin, Wei Ye

“…‘Jian ye’ was the highest. Transcriptome and metabolome data showed that <i>A. roxburghii</i> cv. …”
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Comparative transcriptome analysis reveals candidate gene for flowering time QTL HvHeading in barley by Nazanin P. Afsharyan, Jens Léon, Ali Ahmad Naz, Agim Ballvora

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Combined metabolome and transcriptome to analyze the regulatory network of key enzymes in the synthesis of senkirkine in Emilia sonchifolia by Jinli Yao, Yanqing Qin, Dongping Tu, Yumei Huang, Liuguan Liang, Wenhui Cai, Mingli Huang, Xiaoqi Zhu, Xinling Lao

“…Through qRT-PCR of five key enzyme genes, researchers found that four genes (BAHD-Ats, CCoAOMT, BOMT, 3AT) peaked in roots, while CAD showed highest expression in stems—findings consistent with transcriptomic results. This study provided references for gene functional expression analysis and laid a foundation for decoding the senkirkine biosynthesis pathway. …”
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Integration analysis of transcriptome and proteome of Chinese Merino sheep (Ovis aries) embryonic skeletal muscle by Mian Feng, Wenping Hu, Xinyue Wang, Lulu Liu, Yunhui Liu, Li Zhang

“…In this study, we performed the comprehensive analysis of transcriptome and proteome of Chinese Merino sheep at embryonic ages Day85 (D85N), Day105 (D105N), and Day135 (D135N) by the tandem mass tags (TMT) and RNA‐seq methods. …”
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Heat stress induces specific methylation, transcriptomic and metabolic pattern in dairy cows and their female progeny by Kathrin Halli, Tong Yin, Christian Koch, Stefan Krebs, Sven König

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An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways by Xiaoxia Ma, Yinju Tang, Zedi Feng, Xiu Yin, Yijun Meng, Xiaopu Yin, Tian Xie

“…Summarily, our report provided an organ‐specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.…”
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De Novo transcriptome assembly of Diaprepes abbreviatus: foundations for functional genomics and targeted pest management by Lamiaa M. Mahmoud, Tejbhan Saini, Nabil Killiny

“…De novo transcriptome assembly provides a practical approach for reconstructing the full set of transcripts in organisms without a reference genome, enabling the identification of novel genes and isoforms as well as the study of gene expression patterns. …”
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Solexa-Sequencing Based Transcriptome Study of Plaice Skin Phenotype in Rex Rabbits (Oryctolagus cuniculus). by Lei Pan, Yan Liu, Qiang Wei, Chenwen Xiao, Quanan Ji, Guolian Bao, Xinsheng Wu

“…<h4>Conclusions/significance</h4>The rabbit transcriptome profiling data provide new insights in understanding the molecular mechanisms underlying rabbit skin growth and development.…”
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Physiological and Transcriptome Analyses of Gill and Hepatopancreas of <i>Potamocorbula ustulata</i> Under Ammonia Exposure by Jing He, Xinhui Wang, Mingyu Wu, Zhihua Lin, Lin He, Xiafei Zheng

“…These findings suggest that ammonia stress disrupts antioxidant defense, triggers inflammation and apoptosis, and enhances ammonia tolerance through excretion, glutamine conversion, and urea synthesis. This study provides insights into the molecular mechanisms underlying ammonia tolerance in bivalves.…”
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