Molecular Plant最新文献

{"title":"Phosphorylation/dephosphorylation-mediated regulation of ABI1/2 activity and stability for fine-tuning ABA signaling.","authors":"Mar Bono, Maria Rivera-Moreno, Armando Albert, Pedro L Rodriguez","doi":"10.1016/j.molp.2025.05.006","DOIUrl":"10.1016/j.molp.2025.05.006","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1103-1105"},"PeriodicalIF":17.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A top HAT: A maize mutant hypersusceptible to Agrobacterium transformation.","authors":"Catherine M Doorly, Wout Vandeputte, Inge De Clercq, Laurens Pauwels","doi":"10.1016/j.molp.2025.05.012","DOIUrl":"10.1016/j.molp.2025.05.012","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1115-1117"},"PeriodicalIF":17.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SeedLLM·Rice: A large language model integrated with rice biological knowledge graph.","authors":"Fan Yang, Huanjun Kong, Jie Ying, Zihong Chen, Tao Luo, Wanli Jiang, Zhonghang Yuan, Zhefan Wang, Zhaona Ma, Shikuan Wang, Wanfeng Ma, Xiaoyi Wang, Xiaoying Li, Zhengyin Hu, Xiaodong Ma, Minguo Liu, Xiqing Wang, Fan Chen, Nanqing Dong","doi":"10.1016/j.molp.2025.05.013","DOIUrl":"10.1016/j.molp.2025.05.013","url":null,"abstract":"<p><p>Rice biology research involves complex decision-making, requiring researchers to navigate a rapidly expanding body of knowledge encompassing extensive literature and multiomics data. The exponential increase in biological data and scientific publications presents significant challenges for efficiently extracting meaningful insights. Although large language models (LLMs) show promise for knowledge retrieval, their application to rice-specific research has been limited by the absence of specialized models and the challenge of synthesizing multimodal data integral to the field. Moreover, the lack of standardized evaluation frameworks for domain-specific tasks impedes the effective assessment of model performance. To address these challenges, we introduce SeedLLM·Rice (SeedLLM), a 7-billion-parameter model trained on 1.4 million rice-related publications, representing nearly 98.24% of global rice research output. Additionally, we present a novel human-centric evaluation framework designed to assess LLM performance in rice biology tasks. Initial evaluations demonstrate that SeedLLM outperforms general-purpose models, including OpenAI GPT-4o1 and DeepSeek-R1, achieving win rates of 57% to 88% on rice-specific tasks. Furthermore, SeedLLM is integrated with the Rice Biological Knowledge Graph (RBKG), which consolidates genome annotations for Nipponbare and large-scale synthesis of transcriptomic and proteomic information from over 1800 studies. This integration enhances the ability of SeedLLM to address complex research questions requiring the fusion of textual and multiomics data. To facilitate global collaboration, we provide free access to SeedLLM and the RBKG via an interactive web portal (https://seedllm.org.cn/). SeedLLM represents a transformative tool for rice biology research, enabling unprecedented discoveries in crop improvement and climate adaptation through advanced reasoning and comprehensive data integration.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1118-1129"},"PeriodicalIF":17.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution and functional characterization of a biosynthetic gene cluster for saponin biosynthesis in Sapindaceae.","authors":"Yingxiao Mai, Huimin Hu, Wenjuan Ji, Yaxuan Xiao, Hong Zhou, Zaohai Zeng, Wenshu Lv, Xingling Su, Jiakun Zheng, Jing Xu, Yanwei Hao, Zhenhua Liu, Rui Xia","doi":"10.1016/j.molp.2025.04.013","DOIUrl":"10.1016/j.molp.2025.04.013","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1089-1093"},"PeriodicalIF":17.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overcoming bottlenecks in virus-mediated gene editing in plants.","authors":"Lingran Zhang, Vishal, Manman Hu, Degao Liu","doi":"10.1016/j.molp.2025.06.003","DOIUrl":"10.1016/j.molp.2025.06.003","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1098-1101"},"PeriodicalIF":17.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144285458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Balancing growth with integrity: The tangle between brassinosteroid and FERONIA.","authors":"Yosapol Harnvanichvech, Yuchen Long","doi":"10.1016/j.molp.2025.05.009","DOIUrl":"10.1016/j.molp.2025.05.009","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1112-1114"},"PeriodicalIF":17.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"WD40-protein-mediated crosstalk among three epigenetic marks regulates chromatin states and yield in rice.","authors":"Liwen Yang, Dongwei Li, Weijun Guo, Juqi Song, Chaofan Liu, Hanlin Liu, Cong Li, Xiaofeng Gu","doi":"10.1016/j.molp.2025.05.016","DOIUrl":"10.1016/j.molp.2025.05.016","url":null,"abstract":"<p><p>Although there is increasing understanding of the regulatory effects of particular epigenetic marks, much less is known about how crosstalk among multiple marks affects genetic regulation. Here, we show that Dwarf-related WD40 protein 1 (DRW1) is involved in DNA 6mA demethylation, H3K27 trimethylation, and RNA m⁵C methylation in rice through its respective recruitment of the DNA demethylase AlkB homolog 1 (OsALKBH1), the histone methyltransferase CURLY LEAF (OsCLF), and NOP2/Sun RNA methyltransferase family member 2 (OsNSUN2). Knockout of DRW1 significantly reduces the extent of chromatin occupancy by OsALKBH1, OsCLF, and OsNSUN2, resulting in increased chromatin accessibility and enhanced expression of genes associated with brassinosteroid biosynthesis and signaling. Gene editing at a CAAT-box (ATTGG→ATTGA) and a GATA motif (GATAGGG→GAT) in the DRW1 promoter leads to elevated DRW1 transcription and thereby enhanced rice grain yield and salt tolerance. In field trials, DRW1-overexpressing rice lines displayed yield increases of ∼30.2% (in both normal and saline soils), accompanied by decreases in DNA 6mA and increases in H3K27me3 and RNA m⁵C levels at target genes. Overall, our study uncovers DRW1-mediated crosstalk among three epigenetic marks (DNA 6mA, H3K27me3, and RNA m⁵C) and reveals how this crosstalk controls transcriptional and post-transcriptional regulation to affect rice yield and salt tolerance.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"1143-1157"},"PeriodicalIF":17.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural basis of auxin recognition and transport in plant influx carrier AUX1","authors":"Huiwen Chen, Junping Fan, Cheng Chi, Jun Zhao, Di Wu, Xiaoguang Lei, Xing Wang Deng, Daohua Jiang","doi":"10.1016/j.molp.2025.06.015","DOIUrl":"https://doi.org/10.1016/j.molp.2025.06.015","url":null,"abstract":"Auxin regulates many aspects of plant growth and development, featuring polar auxin transport mediated by auxin efflux and influx carriers. AUX1 is the prominent auxin importer that actively takes up natural and synthetic auxins. However, the precise mechanisms by which AUX1 recognizes and transports auxin remain elusive. Here, we describe the cryo-electron microscopy structures of <ce:italic>Arabidopsis thaliana</ce:italic> AUX1 in apo and auxin-bound forms, revealing the structural basis for auxin recognition. AUX1 assumes the LeuT-like fold in an inward conformation. The auxin analogue 2,4-D is recognized by polar residues in the middle of AUX1. We identify a putative cation site in AUX1, which plays a role in stabilizing the inward-facing conformation. His249 undergoes a large conformational shift, and mutation of it completely abolished transport activity, suggesting a crucial role of His249 in AUX1 gating. Together, this study provides a structural foundation for a deeper comprehension of auxin influx by AUX1-like carriers.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"106 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144515831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Suppression of TaHDA8-mediated lysine deacetylation of TaAREB3 acts as a drought adaptive mechanism in wheat root development","authors":"Zehui Liu, Qun Yang, Xingbei Liu, Jinpeng Li, Lei Zhang, Wei Chu, Jingchen Lin, Debiao Liu, Danyang Zhao, Xiao Peng, Chaowu Zeng, Mingming Xin, Yingyin Yao, Huiru Peng, Zhongfu Ni, Qixin Sun, Zhaorong Hu","doi":"10.1016/j.molp.2025.06.012","DOIUrl":"https://doi.org/10.1016/j.molp.2025.06.012","url":null,"abstract":"Wheat root systems undergo dynamic and adaptive changes to mitigate the adverse effects through elaborate regulatory mechanisms under drought stress. Elucidating and utilizing these mechanisms is highly important for breeding drought resistant wheat varieties. Here, we identify histone deacetylase TaHDA8, as a critical component in regulating wheat root elongation and drought resistance. Under drought stress, TaHDA8 can be finely tuned to alleviate its inhibition of root elongation, thereby adapting to water deficit. Interestingly, the reduction in TaHDA8 protein levels restores the DNA-binding ability of TaAREB3, a positive regulator of root elongation and drought resistance, which depends on the retention of acetylation at K248 and K281 residues. The restored DNA-binding ability of TaAREB3 activates the expression of <ce:italic>TaKOR1</ce:italic>, thus promoting root elongation by regulating cell proliferation in the root meristem. Further studies reveal that natural variations in the <ce:italic>TaKOR1</ce:italic> promoter determine the differences in TaAREB3 binding, and wheat germplasm with TaHDA8-TaAREB3-TaKOR1 regulatory module has been widely selected. Overall, this study reveals how lysine deacetylases regulate drought-responsive root development via non-histone deacetylation, providing genetic resources for improving root architecture and breeding drought-resistant wheat.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"47 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and Population Evidence Uncovers Divergent Improvement of Vegetable Soybean from Grain Soybean","authors":"Na Liu, Wanjie Feng, Guwen Zhang, Pengfei Gao, Lijie Lian, Jing Yuan, Xuantong Liu, Xiaoyu Ni, Huaying Wang, Jinwen Ou, Yaming Gong, Xutong Wang","doi":"10.1016/j.molp.2025.06.009","DOIUrl":"https://doi.org/10.1016/j.molp.2025.06.009","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"147 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}