Current opinion in plant biology最新文献

{"title":"When DNA methylation integrity fails: Lessons from plant aging and tissue culture.","authors":"Yinwei Zeng, Ken Chen, Ben P Williams","doi":"10.1016/j.pbi.2026.102983","DOIUrl":"https://doi.org/10.1016/j.pbi.2026.102983","url":null,"abstract":"<p><p>Plants maintain DNA methylation landscapes with high fidelity. Multiple pathways are coordinated to maintain DNA methylation patterns over many millions of cell divisions, reproductive generations and even evolutionary timescales. As DNA methylation maintenance is typically a robust and accurate process, scenarios in which the fidelity of methylation patterns is compromised represent compelling opportunities to gain a deeper understanding of DNA methylation stability. In this review, we discuss recent research that sheds light on two points of failure for DNA methylation maintenance: plant aging and tissue culture. In both cases, loss of DNA methylation is associated with the activation of transposable elements, potentially causing further genetic instability. We propose that uncovering the precise relationship between epigenetic instability, tissue culture, and somaclonal variation is crucial and timely, as epigenetic and genetic instability in tissue culture undermines the core strategy of gene editing to generate new genetic variants with high precision.</p>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"94 ","pages":"102983"},"PeriodicalIF":7.3,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149223525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Malate synthesis in the chloroplasts of C3 plants","authors":"Arnold J. Bloom","doi":"10.1016/j.pbi.2026.102931","DOIUrl":"10.1016/j.pbi.2026.102931","url":null,"abstract":"<div><div>Vascular plants distribute reducing power among organelles, cells, and tissues in the form of malate, a stable metabolite from which organisms can quickly generate the strong reductants NADH and NADPH. Current thought is that malate in chloroplasts derives either from the import and reduction of oxaloacetate or from the import of malate into chloroplasts via an exchange with glutamate. This article proposes that plastid malate may also derive from rubisco-mediated catabolism of RuBP to pyruvate, followed by the putative conversion of pyruvate to malate through two alternative pathways. One pathway involves the enzymes phosphogluconate dehydrogenase and malic enzyme, and the other involves PEP carboxylase and malate dehydrogenase. These enzymes have metal-binding sites that accommodate either manganese or magnesium, but association with manganese favors malate generation. Therefore, plants may shift the balance between manganese and magnesium activities in chloroplasts to enhance malate generation for nitrate and sulfate assimilation into amino acids at the expense of carbon fixation and carbohydrate accumulation. This regulatory mechanism may help plants maintain protein homeostasis as atmospheric CO₂ rises in the coming decades.</div></div><div>Vascular plants distribute reducing power among organelles, cells, and tissues in the form of malate, a stable metabolite from which organisms can quickly generate the strong reductants NADH and NADPH. Current thought is that malate in chloroplasts derives either from the import and reduction of oxaloacetate or from the import of malate into chloroplasts via an exchange with glutamate. This article proposes that plastid malate may also derive from rubisco-mediated catabolism of RuBP to pyruvate, followed by the putative conversion of pyruvate to malate through two alternative pathways. One pathway involves the enzymes phosphogluconate dehydrogenase and malic enzyme, and the other involves PEP carboxylase and malate dehydrogenase. These enzymes have metal-binding sites that accommodate either manganese or magnesium, but association with manganese favors malate generation. Therefore, plants may shift the balance between manganese and magnesium activities in chloroplasts to enhance malate generation for nitrate and sulfate assimilation into amino acids at the expense of carbon fixation and carbohydrate accumulation. This regulatory mechanism may help plants maintain protein homeostasis as atmospheric CO₂ rises in the coming decades.</div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"92 ","pages":"Article 102931"},"PeriodicalIF":7.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polyploid genome evolution across land plants: Progress and perspectives","authors":"Hanna Weiss-Schneeweiss,&nbsp;Gerald M. Schneeweiss,&nbsp;Norman J. Wickett","doi":"10.1016/j.pbi.2025.102857","DOIUrl":"10.1016/j.pbi.2025.102857","url":null,"abstract":"<div><div>The enormous wealth of data on the incidence of polyploidy and its significance for genome evolution in angiosperms has greatly advanced our understanding of plant evolution. This has enabled the identification of correlations between polyploidization and life history trait evolution as well as unraveling the complex interplay between genome multiplication and the biology of individual lineages giving rise to intricate and unique patterns of genome evolution despite shared evolutionary processes. Advances in sequencing and analytical methods result in the quickly increasing representation of other land plant lineages, such as bryophytes or ferns. These data continue to reveal that the levels of genome evolution complexity known from angiosperms are to be found across all land plants, albeit to lineage-specific extents. Greatly expanded taxonomic sampling across land plants will not only deepen our understanding of the interplay between polyploidy and the evolution of traits and life histories, e.g. in the context of the conquest of land, but also will allow an evolutionarily broader assessment of the role of polyploidy in shaping genome dynamics.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"90 ","pages":"Article 102857"},"PeriodicalIF":7.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146075907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding plant cell heterogeneity and dynamics across responses, development, to evolution with single-cell technologies","authors":"Dongbo Shi ,&nbsp;Keiko Sugimoto ,&nbsp;Kenji Fukushima","doi":"10.1016/j.pbi.2025.102854","DOIUrl":"10.1016/j.pbi.2025.102854","url":null,"abstract":"<div><div>Single-cell technologies are redefining plant cell identity. Traditional classifications based on position, morphology, and a few marker genes yielded static, coarse cell categories. In contrast, single-cell and single-nucleus RNA sequencing reveal hidden cellular heterogeneity and reconstruct developmental trajectories in ostensibly well-characterized plant tissues including vasculature and mesophyll. Environmental cues such as pathogen attack, drought, and wounding generate transient, spatially restricted cell states that bulk profiling masks, and these dynamics are best resolved by integrating single-cell data with spatial transcriptomics and live imaging. Comparative single-cell analyses extend these insights across evolution, revealing conserved core cell-type groups, lineage-specific innovations, and rapid transcriptomic rewiring in particular cell types. Emerging computational strategies mitigate orthology issues caused by genome duplications, enabling robust cross-species atlas alignment. These advances demonstrate that plant cell identity is dynamic, context-dependent, and distributed along continuous spectra. We argue that future frameworks should balance discrete cell-type labels with flexible state-based descriptions and integrate multiomic and spatial information to capture the full plasticity of plant cells, from ephemeral stress responses to millennial evolutionary changes.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"90 ","pages":"Article 102854"},"PeriodicalIF":7.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146006761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The potential of plant palaeogenomic research","authors":"Jazmín Ramos-Madrigal","doi":"10.1016/j.pbi.2025.102856","DOIUrl":"10.1016/j.pbi.2025.102856","url":null,"abstract":"<div><div>Plant palaeogenomics has transformed the way we study plant evolution. After a slow start, the last decade has seen a shift from the study of a few genomic markers to genome-wide data and complete genomes across multiple species. These studies have changed fundamental ideas about plant domestication and evolution.</div><div>The field still has great potential to unlock. Emerging approaches promise to recover genomic information from both plants and their associated microbes from macrobotanical remains, providing a new perspective to study deep-time plant-microbiome coevolution. Environmental DNA preserved in ancient sediments may soon yield complete plant genomes, expanding our ability to study population dynamics well before the rise of agriculture. Ancient genomes also provide a reservoir of lost genetic diversity that we could exploit to improve crop resilience and adaptation.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"90 ","pages":"Article 102856"},"PeriodicalIF":7.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146075905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NLR receptor subcellular localization and plant immune activation","authors":"Di Liang ,&nbsp;Li Huang ,&nbsp;Dehe Zhu ,&nbsp;Yiwen Deng ,&nbsp;Zuhua He","doi":"10.1016/j.pbi.2025.102855","DOIUrl":"10.1016/j.pbi.2025.102855","url":null,"abstract":"<div><div>Nucleotide-binding and leucine-rich repeat receptor (NLR) proteins serve as cornerstone components of the plant immune system, typically recognizing pathogen effector proteins to assemble resistance complexes (resistosomes) that trigger robust immune responses. As pivotal targets for crop disease resistance breeding, NLRs have been shown to exhibit subcellular localization-dependent functional regulation, influencing processes including effector recognition, immune complex assembly, and activation of downstream signaling pathways. Here, we review the distinct subcellular compartmentalization patterns of NLR proteins and their mechanistic roles in orchestrating plant disease resistance.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"90 ","pages":"Article 102855"},"PeriodicalIF":7.5,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146006762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging cells and stages: Plasmodesmata for the coordination of plant development","authors":"Elmehdi Bahafid ,&nbsp;Zoe Kathleen Barr ,&nbsp;Rebecca Corinna Burkart ,&nbsp;Rosanna Petrella ,&nbsp;Rüdiger Simon","doi":"10.1016/j.pbi.2025.102843","DOIUrl":"10.1016/j.pbi.2025.102843","url":null,"abstract":"<div><div>Plants are multicellular organisms in which numerous specialized cell types must communicate to function as a unified system. Plant cells are enclosed by rigid walls, and therefore, intercellular communication requires the presence of plasmodesmata (PD), cytoplasmic channels bridging neighboring cells. These structures are crucial for coordinating developmental stages across tissues. To ensure proper growth and development, the movement of signaling molecules, RNAs, proteins, and nutrients through PD must be tightly controlled, underscoring the importance of regulating their selectivity.</div><div>Despite their essential role, direct evidence for PD involvement in developmental processes is limited and the mechanisms governing PD regulation remain incompletely understood. Recent studies suggest the existence of diverse regulatory mechanisms beyond the classical callose-based model, revealing a likely complex interplay of several PD regulators across development. In this review, we summarize recent findings on the role of PD in various plant developmental programs, discuss emerging regulatory mechanisms, and highlight how much remains to be discovered.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102843"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145786440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"mRNA methylation at the crossroads of translation, transport, and decay in plant development and stress responses","authors":"Yihan Dong ,&nbsp;Wenna Zhang ,&nbsp;Veli Vural Uslu","doi":"10.1016/j.pbi.2025.102851","DOIUrl":"10.1016/j.pbi.2025.102851","url":null,"abstract":"<div><div>Modified nucleotides on RNAs have been investigated for over six decades for their potential role in regulating gene expression and protein synthesis across a wide range of organisms, from animals to plants and fungi, as well as in viral genetic materials. Among them, mRNA methylation stands out with its dynamic nature, which underscores the adaptability of the epitranscriptome in developmental transitions and response to environmental stress, especially in plants. Advances in next-generation sequencing methods have revealed the specific sequence contexts of mRNA methylation, uncovering their involvement in gene regulatory networks. Additionally, genetic perturbations on the writers, erasers, and readers of m⁶A and m⁵C expanded our understanding of the physiological function and the mode of action of these modifications. In this review, we highlight recent advances in understanding how mRNA fate decisions, mainly determined by m⁶A and m⁵C RNA methylation, shape stress response and development in plants.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102851"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145920658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-coding regulation in seasonal flowering control – Insights from FLC","authors":"Mélanie Ormancey,&nbsp;Julia I. Qüesta","doi":"10.1016/j.pbi.2025.102831","DOIUrl":"10.1016/j.pbi.2025.102831","url":null,"abstract":"<div><div>As sessile organisms, plants must adapt to fluctuating environmental conditions, with temperature serving as a key driver of developmental transitions. The ability to accurately perceive and respond to seasonal temperature fluctuations is critical for plant survival and reproductive success. In many species, prolonged exposure to the low temperatures of autumn and winter triggers vernalization, enabling flowering to occur under favourable spring conditions. This process has been extensively characterized in <em>Arabidopsis thaliana</em>, particularly through studies of the floral repressor <em>FLOWERING LOCUS C</em> (<em>FLC</em>). In this mini review, we summarize recent advances in understanding the genetic basis of vernalization, focusing on how non-coding polymorphisms influence <em>FLC</em> transcript accumulation and expression of long non-coding RNAs, thereby altering vernalization requirement and efficiency. Variation in the quantitative expression of <em>FLC</em> and its homologs has shaped the evolution of diverse life-history strategies of Arabidopsis relatives within the Brassicaceae family. Dissecting how naturally occurring non-coding variants reconfigure the cis-regulatory landscape of <em>FLC</em>-like genes will be key to understanding the molecular basis of phenological diversity. Such insights not only illuminate the evolutionary dynamics of flowering time control but also holds promise to provide targets for crop improvement under changing climatic conditions.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102831"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene expression scaling with cell size: Insights across kingdoms","authors":"Alejandro Fonseca,&nbsp;Stefanie Rosa","doi":"10.1016/j.pbi.2025.102852","DOIUrl":"10.1016/j.pbi.2025.102852","url":null,"abstract":"<div><div>Gene expression is typically studied on a gene-by-gene basis, with regulation analyzed primarily in response to environmental or developmental cues. In contrast, much less is known about how intrinsic factors, such as cell size or DNA content, influence global gene expression patterns. Cell size varies significantly across different cell types and dynamically changes during the cell cycle. To maintain proper intracellular concentrations of biomolecules such as mRNAs and proteins, gene expression must be coordinated with cell size. Emerging evidence from diverse organisms, including bacteria, yeast, animals, and plants, demonstrates that transcriptional output scales with cell size, suggesting a conserved principle of gene regulation. However, the mechanisms by which cells sense their size and modulate gene expression accordingly remain poorly understood. In this review, we summarize recent advances in uncovering the molecular and cellular principles of gene expression scaling with cell size across kingdoms. We also highlight key open questions in the field, with a particular emphasis on how plant systems, still underexplored in this context, can provide additional insights into the fundamental principles of size-dependent gene regulation.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102852"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145965409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}