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Annual review of plant biology最新文献

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What Are We Learning from Plant Pangenomes? 我们从植物泛基因组学到了什么？
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2024-12-02 DOI: 10.1146/annurev-arplant-090823-015358
Murukarthick Jayakodi, Hyeonah Shim, Martin Mascher
{"title":"What Are We Learning from Plant Pangenomes?","authors":"Murukarthick Jayakodi, Hyeonah Shim, Martin Mascher","doi":"10.1146/annurev-arplant-090823-015358","DOIUrl":"10.1146/annurev-arplant-090823-015358","url":null,"abstract":"<p><p>A single reference genome does not fully capture species diversity. By contrast, a pangenome incorporates multiple genomes to capture the entire set of nonredundant genes in a given species, along with its genome diversity. New sequencing technologies enable researchers to produce multiple high-quality genome sequences and catalog diverse genetic variations with better precision. Pangenomic studies have detected structural variants in plant genomes, dissected the genetic architecture of agronomic traits, and helped unravel molecular underpinnings and evolutionary origins of plant phenotypes. The pangenome concept has further evolved into a so-called super-pangenome that includes wild relatives within a genus or clade and shifted to graph-based reference systems. Nevertheless, building pangenomes and representing complex structural variants remain challenging in many crops. Standardized computing pipelines and common data structures are needed to compare and interpret pangenomes. The growing body of plant pangenomics data requires new algorithms, huge data storage capacity, and training to help researchers and breeders take advantage of newly discovered genes and genetic variants.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"663-686"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765846","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}
引用次数: 0
From Starfish to Gibberellins: Biosynthesis and Regulation of Plant Hormones. 从海星到赤霉素：植物激素的生物合成和调控。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2024-12-11 DOI: 10.1146/annurev-arplant-083023-032239
Yuji Kamiya
{"title":"From Starfish to Gibberellins: Biosynthesis and Regulation of Plant Hormones.","authors":"Yuji Kamiya","doi":"10.1146/annurev-arplant-083023-032239","DOIUrl":"10.1146/annurev-arplant-083023-032239","url":null,"abstract":"<p><p>I grew up with laboratory glassware and microscopes as treasures from a young age. I was a member of the Chemistry Club in junior high school, and when I visited RIKEN with club members, I wished to become an organic chemist in the future. I received my doctoral degree through the study of the spawning inhibitor of starfish. I became a researcher at RIKEN and identified the chemical structure of a mating pheromone of a yeast. As a plant biochemist, I studied a cell-free system of gibberellins at the University of Göttingen and tried to identify the gibberellin biosynthetic pathways in plants and clone gibberellin biosynthetic enzyme genes to understand the light regulation of plant growth. I also worked on biosynthetic enzymes of abscisic acid, indole acetic acid, and brassinosteroids. I developed a special interest in the oxygenases of plant hormone biosynthesis, cytochrome P450 monooxygenases, 2-oxoglutarate-dependent dioxygenase, molybdenum cofactor-containing oxidase, and flavin-containing monooxygenase.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"1-24"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811989","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}
引用次数: 0
Monkeys at Rigged Typewriters: A Population and Network View of Plant Immune System Incompatibility. 操纵打字机的猴子：植物免疫系统不相容的种群和网络观点。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-03 DOI: 10.1146/annurev-arplant-083023-041225
Rachelle R Q Lee, Eunyoung Chae
{"title":"Monkeys at Rigged Typewriters: A Population and Network View of Plant Immune System Incompatibility.","authors":"Rachelle R Q Lee, Eunyoung Chae","doi":"10.1146/annurev-arplant-083023-041225","DOIUrl":"10.1146/annurev-arplant-083023-041225","url":null,"abstract":"<p><p>Immune system incompatibilities between naturally occurring genomic variants underlie many hybrid defects in plants and present a barrier for crop improvement. In this review, we approach immune system incompatibilities from pan-genomic and network perspectives. Pan-genomes offer insights into how natural variation shapes the evolutionary landscape of immune system incompatibilities, and through it, selection, polymorphisms, and recombination resistance emerge as common features that synergistically drive these incompatibilities. By contextualizing incompatibilities within the immune network, immune receptor promiscuity, complex dysregulation, and single-point failure appear to be recurrent themes of immune system defects. As geneticists break genes to investigate their function, so can we investigate broken immune systems to enrich our understanding of plant immune systems and work toward improving them.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"523-550"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603719","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}
引用次数: 0
Phytomelatonin: Biosynthesis, Signaling, and Functions. 植物褪黑素：生物合成、信号传递和功能。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-14 DOI: 10.1146/annurev-arplant-053124-045147
Qi Chen, Yanli Chen, Xue Li, Liping Zhang, Zed Rengel
{"title":"Phytomelatonin: Biosynthesis, Signaling, and Functions.","authors":"Qi Chen, Yanli Chen, Xue Li, Liping Zhang, Zed Rengel","doi":"10.1146/annurev-arplant-053124-045147","DOIUrl":"10.1146/annurev-arplant-053124-045147","url":null,"abstract":"<p><p>Phytomelatonin has attracted significant attention over the years for its roles in promoting plant growth and enhancing stress resistance. The biosynthetic pathway of phytomelatonin is more intricate than that of melatonin in animals, occurring in plants in the endoplasmic reticulum, chloroplasts, mitochondria, and cytoplasm. By compartmentalizing phytomelatonin production within specific organelles and differentially expressing biosynthesis genes, plants may finely tune the levels of this hormone under normal growth conditions, as well as in rapid responses to changing environmental conditions. Phytomelatonin can interact with its receptor PMTR1, triggering G protein signaling, initiating ROS-Ca2+ signaling hubs, and activating MAPK cascades. Phytomelatonin's main role is promoting plant growth and development, whereas phytomelatonin-mediated resistance to numerous abiotic and biotic stresses is inducible and primed. The flexibility in the biosynthesis, together with the signaling pathways influenced, may contribute to phytomelatonin balancing the trade-offs between growth and stress resistance.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"171-195"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630122","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}
引用次数: 0
Green Revolution DELLA Proteins: Functional Analysis and Regulatory Mechanisms. 绿色革命DELLA蛋白质：功能分析和调控机制。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2024-12-02 DOI: 10.1146/annurev-arplant-053124-050732
David Alabadí, Tai-Ping Sun
{"title":"Green Revolution DELLA Proteins: Functional Analysis and Regulatory Mechanisms.","authors":"David Alabadí, Tai-Ping Sun","doi":"10.1146/annurev-arplant-053124-050732","DOIUrl":"10.1146/annurev-arplant-053124-050732","url":null,"abstract":"<p><p>The <i>DELLA</i> genes, also referred to as Green Revolution genes, encode conserved master growth regulators in plants. The nuclear-localized DELLA proteins are transcription regulators that interact with hundreds of transcription factors and other transcription regulators. They not only function as gibberellin signaling repressors in vascular plants but also play a central role in coordinating diverse signaling pathways in response to both internal hormonal signals and external cues (e.g., light and nutrient conditions, biotic and abiotic stresses). Through a combination of genetic, genomic, biochemical, and structural studies, significant advances have been made in understanding both the functional domains and motifs within DELLAs and the molecular mechanisms underlying their function. Here, we highlight new insights into the molecular workings of DELLA proteins, including an evolutionary perspective.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"373-400"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096672/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants. 植物DNA甲基化的建立、维持和去除的分子机制。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-03 DOI: 10.1146/annurev-arplant-083123-054357
Guohui Xie, Xuan Du, Hongmiao Hu, Jiamu Du
{"title":"Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants.","authors":"Guohui Xie, Xuan Du, Hongmiao Hu, Jiamu Du","doi":"10.1146/annurev-arplant-083123-054357","DOIUrl":"10.1146/annurev-arplant-083123-054357","url":null,"abstract":"<p><p>Methylation at the fifth position of the cytosine base (5mC) is a critical DNA modification with important functions in gene silencing, genome imprinting, and suppression of transposable elements in eukaryotes. Biochemically, DNA methylation is dynamically regulated by three critical processes: the de novo establishment of DNA methylation, the maintenance of DNA methylation by preexisting methylation patterns, and the removal of DNA methylation. In plants, DNA methylation is very complex with unique features. In past decades, a series of biochemical and structural studies, especially empowered by the recent breakthroughs of high-resolution cryogenic electron microscopy, have helped uncover the molecular mechanisms underlying the establishment, maintenance, and removal of DNA methylation in plants. This review summarizes recent research advances in these three aspects of DNA methylation and lays out a molecular view of plant DNA methylation from biochemical and structural perspectives.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"143-170"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Dynamics, Degradation, and Afterlives of Pectins: Influences on Cell Wall Assembly and Structure, Plant Development and Physiology, Agronomy, and Biotechnology. 果胶的动态、降解和寿命：对细胞壁组装和结构、植物发育和生理、农学和生物技术的影响。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-01-22 DOI: 10.1146/annurev-arplant-083023-034055
Charles T Anderson, Jérôme Pelloux
{"title":"The Dynamics, Degradation, and Afterlives of Pectins: Influences on Cell Wall Assembly and Structure, Plant Development and Physiology, Agronomy, and Biotechnology.","authors":"Charles T Anderson, Jérôme Pelloux","doi":"10.1146/annurev-arplant-083023-034055","DOIUrl":"10.1146/annurev-arplant-083023-034055","url":null,"abstract":"<p><p>Pectins underpin the assembly, molecular architecture, and physical properties of plant cell walls and through their effects on cell growth and adhesion influence many aspects of plant development. They are some of the most dynamic components of plant cell walls, and pectin remodeling and degradation by pectin-modifying enzymes can drive developmental programming via physical effects on the cell wall and the generation of oligosaccharides that can act as signaling ligands. Here, we introduce pectin structure and synthesis and discuss pectin functions in plants. We highlight recent advances in understanding the structure-function relationships of pectin-modifying enzymes and their products and how these advances point toward new approaches to bridging key knowledge gaps and manipulating pectin dynamics to control plant development. Finally, we discuss how a deeper understanding of pectin dynamics might enable innovations in agronomy and biotechnology, unlocking new benefits from these ubiquitous but complex polysaccharides.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"85-113"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021641","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}
引用次数: 0
Between Host and Invaders: The Subcellular Cell Wall Dynamics at the Plant-Pathogen Interface. 寄主与入侵者之间：植物-病原体界面的亚细胞细胞壁动力学。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 DOI: 10.1146/annurev-arplant-061824-115733
Lucrezia Pinto, Luis Soler-López, Antonio Serrano, Clara Sánchez-Rodríguez
{"title":"Between Host and Invaders: The Subcellular Cell Wall Dynamics at the Plant-Pathogen Interface.","authors":"Lucrezia Pinto, Luis Soler-López, Antonio Serrano, Clara Sánchez-Rodríguez","doi":"10.1146/annurev-arplant-061824-115733","DOIUrl":"10.1146/annurev-arplant-061824-115733","url":null,"abstract":"<p><p>Plant-pathogen interactions have profound ecological implications and are crucial for food security. Usually studied at the two extreme scales of plant organ symptomatology and host-microbe molecules, they are a cell-cell event mainly occurring at the subcellular level of the plant apoplast. Here, the cell walls of both organisms suffer an intense alteration as a consequence of active degradation by the opponent and self-protection mechanisms to survive and continue growing. The plant cell wall modifications and their role in defense as danger signals and activators of signaling cascades have been studied for a few decades, mainly at the organ plane. Still, much remains unknown about this process, including cellular and subcellular minority decorations, proteins, and mechanical cues. Comparatively, the microbial cell wall changes in planta are virtually unexplored. By investigating the interface between plant and microbial cell walls biochemically, structurally, and mechanically, we aim to highlight the dynamic interplay in these subcellular areas and its significance for the host-invader interaction.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"76 1","pages":"255-284"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109292","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}
引用次数: 0
Root Growth and Development in "Real Life": Advances and Challenges in Studying Root-Environment Interactions. 现实生活中的根系生长和发育：研究根系与环境相互作用的进展与挑战》。
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-14 DOI: 10.1146/annurev-arplant-083123-074506
Poonam Mehra, Jason Banda, Lucas León Peralta Ogorek, Riccardo Fusi, Gabriel Castrillo, Tino Colombi, Bipin K Pandey, Craig J Sturrock, Darren M Wells, Malcolm J Bennett
{"title":"Root Growth and Development in \"Real Life\": Advances and Challenges in Studying Root-Environment Interactions.","authors":"Poonam Mehra, Jason Banda, Lucas León Peralta Ogorek, Riccardo Fusi, Gabriel Castrillo, Tino Colombi, Bipin K Pandey, Craig J Sturrock, Darren M Wells, Malcolm J Bennett","doi":"10.1146/annurev-arplant-083123-074506","DOIUrl":"10.1146/annurev-arplant-083123-074506","url":null,"abstract":"<p><p>Plant roots play myriad roles that include foraging for resources in complex soil environments. Within this highly dynamic soil environment roots must sense, interact with, and acclimate to factors such as water availability, microbiota, and heterogeneous distribution of nutrients. To aid their acclimation, roots alter their growth and development to optimize their architecture and actively regulate the physical, chemical, and biological properties of their rhizosphere. Understanding the complex interactions between roots and rhizosphere is critical for designing future crops with improved root traits better adapted to diverse and challenging soil conditions. However, studying roots and their interactions with soil under real-world conditions presents significant challenges. Addressing these challenges demands developing realistic laboratory-based model systems and innovative field-based root imaging techniques. Our review surveys the current knowledge and recent advances in understanding root-environment interactions while proposing future solutions to study roots under more \"real-life\" soil conditions.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"467-492"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630124","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}
引用次数: 0
RNA Structure: Function and Application in Plant Biology. RNA 结构：植物生物学中的功能和应用
IF 26.5 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-18 DOI: 10.1146/annurev-arplant-083123-055521
Huakun Zhang, Yiliang Ding
{"title":"RNA Structure: Function and Application in Plant Biology.","authors":"Huakun Zhang, Yiliang Ding","doi":"10.1146/annurev-arplant-083123-055521","DOIUrl":"10.1146/annurev-arplant-083123-055521","url":null,"abstract":"<p><p>RNA orchestrates intricate structures that influence gene expression and protein production in all living organisms, with implications for fundamental biology, medicine, and agriculture. Although extensive research has been conducted on RNA biology, many regulatory mechanisms remain elusive due to the complex and dynamic nature of RNA structures and past technological limitations. Recent advancements in RNA structure technology have revolutionized plant RNA biology research. Here, we review cutting-edge technologies for studying RNA structures in plants and their functional significance in diverse biological processes. Additionally, we highlight the pivotal role of RNA structure in influencing plant growth, development, and responses to environmental stresses. We also discuss the potential evolutionary significance of RNA structure in natural adaptation and crop domestication. Finally, we propose leveraging RNA structure-mediated gene regulation as an innovative strategy to bolster plant resilience against climate change.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"115-141"},"PeriodicalIF":26.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656162","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}
引用次数: 0
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