Molecular Plant最新文献

{"title":"ERFVIIs as transducers of oxygen-sensing in the evolution of land plant response to hypoxia.","authors":"Laura Dalle Carbonare, Hans van Veen, Vinay Shukla, Monica Perri, Liem Bui, Michael J Holdsworth, Francesco Licausi","doi":"10.1016/j.molp.2025.05.015","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.015","url":null,"abstract":"<p><p>The transcriptional response to low oxygen (hypoxia) in flowering plants is transduced through group VII Ethylene Response Factor (ERFVII) transcription factors, whose proteolysis is oxygen-dependent via the PLANT CYSTEINE OXIDASE (PCO) N-degron pathway. When and how this response to hypoxia evolved in land plants remains unknown. Here we investigated the conservation and divergence of transcriptional responses to hypoxia in major land plant clades. We identified induction of gene functions associated with glycolysis and fermentation as part of a conserved response across all land plant divisions. Our results indicate that ERFVIIs appeared in the last common ancestor of vascular plants with true roots, concurrently with oxygen-dependent destabilisation, to regulate hypoxia-adaptive genes. Proteins from other ERF groups have been recruited multiple times in different clades as substrates of the PCO N-degron pathway. Our results demonstrate that the response of land plants to hypoxia has been refined in derived clades through the evolution of ERFVIIs as transcriptional transducers, that occurred concomitantly with the appearance of vascular systems and roots as foraging systems through hypoxic soil.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174189","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, Xi-Qing Wang, Fan Chen, Nanqing Dong","doi":"10.1016/j.molp.2025.05.013","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.013","url":null,"abstract":"<p><p>Rice biology research involves complex decision-making, requiring researchers to navigate a vast and growing body of knowledge that includes extensive literature and multiomics data. The exponential increase in biological data and scientific publications has posed significant challenges in efficiently extracting meaningful insights. While large language models (LLMs) show promise for knowledge retrieval, their application to rice-specific research is hindered 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 assessment of model performance in this area. To address these challenges, we introduce SeedLLM·Rice (SeedLLM), a 7-billion-parameter model trained using 1.4 million rice-related publications, which represent nearly 98.24% of global rice research. Additionally, we present a novel human evaluation framework designed to assess LLM performance in rice biology tasks. Initial evaluations of rice-specific tasks demonstrate that SeedLLM outperforms general-purpose models such as OpenAI GPT-4o1 and DeepSeek-R1, achieving win rates ranging from 57% to 88%. 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 1,800 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, facilitating unprecedented discoveries in crop improvement and climate adaptation through its advanced reasoning capabilities and comprehensive data integration.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-28","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":"Pan-genome and Haplotype Map of Cassava Cultivars and Wild Ancestors Provide Insights into its Adaptive Evolution and Domestication.","authors":"Zhiqiang Xia, Zhenglin Du, Xincheng Zhou, Sirong Jiang, Tingting Zhu, Le Wang, Fei Chen, Luiz Carvalho, Meiling Zou, Luis Augusto Becerra López-Lavalle, Xiaofei Zhang, Liangye Xu, Zhenyu Wang, Meili Chen, Xin Guo, Shujuan Wang, Mengtao Li, Yuanchao Li, Haiyan Wang, Shisheng Liu, Yuting Bao, Long Zhao, Chenji Zhang, Jianjia Xiao, Fengguang Guo, Xu Shen, Haozheng Li, Cheng Lu, Fei Qiao, Hernan Ceballos, Huabing Yan, Xiaochun Qin, Ling Ma, Huaifang Zhang, Shuang He, Wenming Zhao, Yinglang Wan, Yinhua Chen, Dongyi Huang, Kaimian Li, Bin Liu, Ming Peng, Weixiong Zhang, Birger Lindberg Møller, Xin Chen, Ming-Cheng Luo, Jingfa Xiao, Wenquan Wang","doi":"10.1016/j.molp.2025.05.014","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.014","url":null,"abstract":"<p><p>Cassava is an important, resilient tropical crop that produces large starchy storage roots and high biomass. But how did cassava´s remarkable environmental adaptability and key economic traits evolve from its wild species? We constructed nearly T2T genomes and their haplotype forms for the cultivar AM560, wild ancestors FLA4047 and W14, a graphic pan-genome of 30 representatives with 1.15 Gb, and built a clarified evolutionary tree of 486 accessions. A comparison of structural variations (SVs) and single-nucleotide variations (SNVs) between the ancestors and cultivated cassavas reveals predominant expansions and contractions of genes and gene families, which are mainly driven by transposons. Significant selective sweeping occurred in 122 footprints of genomes and affects 1,519 domesticated genes. We identify selective mutations in MeCSK and MeFNR2 that could promote photoreactions associated with MeNADP-ME in C₄ photosynthesis in modern cassava. Co-evolution of retard floral primordia and initiation of storage roots may arise from MeCOL5 variants with altered bindings to MeFT1, MeFT2, and MeTFL2. Mutations of MeMATE1 and MeGTR occur in sweet cassava, and MeAHL19 has evolved to regulate the biosynthesis, transport, and endogenous remobilization of cyanogenic glucosides in cassava. These extensive genomic and gene resources provided here and the findings of the evolutionary mechanisms responsible for beneficial traits in modern cultivars represent a stepping-stone in future breeding of cassava.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174190","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 Doorly, Wout Vandeputte, Inge De Clercq, Laurens Pauwels","doi":"10.1016/j.molp.2025.05.012","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.012","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-26","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":"A plant virus causes symptoms through the deployment of a host-mimicking protein domain to attract the insect vector.","authors":"Man Gao, Emmanuel Aguilar, Borja Garnelo Gómez, Laura Medina-Puche, Pengfei Fan, Irene Ontiveros, Shaojun Pan, Huang Tan, Hua Wei, Edda von Roepenack-Lahaye, Na Chen, Xiao-Wei Wang, David C Baulcombe, Eduardo R Bejarano, Juan Antonio Díaz-Pendón, Masahiko Furutani, Miyo Terao Morita, Rosa Lozano-Durán","doi":"10.1016/j.molp.2025.05.011","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.011","url":null,"abstract":"<p><p>Plant viruses cause symptoms with devastating consequences for agriculture. However, the molecular mechanisms underlying symptom development in viral infections remain largely unexplored. Here, we show that tomato yellow leaf curl virus (TYLCV) interferes with host developmental programs through a host-mimicking domain present in the viral C4 protein. This domain mediates the interaction between C4 and a family of RCC1-like domain-containing (RLD) proteins, previously shown to be required for proper plant development and environmental responses. C4 outcompetes an endogenous interactor of RLDs, hijacking RLD proteins to the plasma membrane and disrupting their function in orchestrating endomembrane trafficking and polar auxin transport. Strikingly, symptoms do not affect viral accumulation in the plant, but serve as attractants for the insect vector, presumably promoting pathogen spread in an ecological context. Our work sheds light on the molecular underpinnings and biological relevance of symptom development triggered by TYLCV in tomato. Since most plant viruses are insect-transmitted, the principles described here might have broad applicability to crop-virus interactions.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151334","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":"Seed dormancy and germination in rice: Molecular regulatory mechanisms and breeding application.","authors":"Fan Xu, Hideki Yoshida, Chengcai Chu, Makoto Matsuoka, Jian Sun","doi":"10.1016/j.molp.2025.05.010","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.010","url":null,"abstract":"<p><p>The transition from dormancy to germination marks the initial stage of the plant life cycle, with its intensity, synchronicity, and timing being critical for crop growth, development, and adaptation to complex climate conditions. This review synthesizes the recent advances with classic molecular mechanisms of dormancy and germination, including their environmental responses and signaling cascades. We integrate these independent studies to provide a comprehensive perspective on the complex regulatory networks and discuss novel insights into how rice seeds perceive and respond to environmental cues during this transition, particularly focusing on stress tolerance to temperature and flooding. Our aim is to bridge the understanding of the molecular mechanisms of dormancy and germination with their breeding applications. Specifically, we discussed gene targets and feasible strategies for the genetic improvement of pre-harvest sprouting (PHS) and direct-seeded rice (DSR), two key traits essential for climate resilience, both of which involve dormancy and germination. Finally, we propose the concept of engineering germination-smart varieties (GSVs) endowed with intelligent environmental adaption.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151348","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":"Potatome - harnessing natural variation of potatoes.","authors":"Delphine Van Inghelandt, Benjamin Stich","doi":"10.1016/j.molp.2025.05.008","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.008","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136379","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":"https://doi.org/10.1016/j.molp.2025.05.009","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-23","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":"A novel NF-Ys-QT12-IRE1 module controlling grain quality and yield thermotolerance in rice.","authors":"Bowen Yang, Yongyao Xie, Yaoguang Liu","doi":"10.1016/j.molp.2025.05.007","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.007","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079144","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":"GAIN: a long-term maize germplasm innovation plan.","authors":"Yang Wang, Peng Zhang, Yingjie Xiao, Hai-Jun Liu, Junqiang Ding, Yanzhi Qu, Jionghao Gao, Wenlong Li, Xiangyang Guo, Angui Wang, Wenqiang Li, Gengshen Chen, Cheng-Qiao Shi, Jie Liu, Jianxiao Liu, Jian Zhang, Jieting Xu, Han Zhang, Jianan Zhang, Jiuran Zhao, Jihua Tang, Haiyang Wang, Zuxin Zhang, Zehui Chen, Jianbing Yan","doi":"10.1016/j.molp.2025.05.005","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.005","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079146","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}