Clémentine Coroenne , Charlotte Lecuyer , Antoine Martin, Sandra Cortijo
{"title":"Individual variability in plants: From intra- to inter-individual variability and its response to the environment","authors":"Clémentine Coroenne , Charlotte Lecuyer , Antoine Martin, Sandra Cortijo","doi":"10.1016/j.pbi.2025.102833","DOIUrl":"10.1016/j.pbi.2025.102833","url":null,"abstract":"<div><div>Individual variability refers to the differences observed among genetically identical plants or cells grown in the same environment. Phenotypic and transcriptional variability have been extensively described in unicellular organisms and mammalian cells. However, increasing evidence now points to both intra- and inter-individual variability in plants. Cell-to-cell variability in gene expression within a single plant (intra-individual variability) is now recognised as a key factor contributing to the robustness of plant development as well as environmental responses. At a broader scale, multiple studies strongly suggest that inter-individual variability, often involving gene expression differences between individual seedlings, can be associated with an adaptive value at the population level under challenging environmental conditions. This review first aims to describe what is currently known about intra- and inter-individual variability in plants, with a main focus on gene expression variation and highlighting the importance of chromatin modifications. We then illustrate how the extent of individual variability can differ depending on environmental conditions, and discuss how the plasticity of such variability may enhance the ability of plants to respond to challenging situations. These observations finally underline the relevance of investigating individual variability in the context of agriculture.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102833"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733635","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":"Cross-kingdom gene transfer as a driver of land plant evolution","authors":"Arie Fridrich, Nicholas A.T. Irwin","doi":"10.1016/j.pbi.2025.102850","DOIUrl":"10.1016/j.pbi.2025.102850","url":null,"abstract":"<div><div>Land plant evolution has been marked by bursts of novelty, often underpinned by extensive genomic innovation. A key mechanism driving these changes is horizontal gene transfer (HGT), the process by which genes move between species and even across taxonomic kingdoms. HGT can accelerate evolutionary change through the rapid introduction of new genes yet its importance in plant biology is only beginning to be understood. Here, we review the functional contributions of HGT during the origin and diversification of land plants. We discuss the occurrence of HGT throughout plant evolution and its impact on the origin of defining traits from cell walls to developmental programs. Beyond ancient contributions, HGT continues to drive the emergence of lineage-specific innovations. Recently acquired bacterial and fungal genes make complex functional contributions to processes including stress response, pathogen defence, and development across plant phylogeny. These observations suggest that HGT was, and continues to be, a major force shaping plant evolution, exemplifying the potential significance of HGT in eukaryotic biology more broadly.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102850"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836624","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 functions of long noncoding RNAs in plants","authors":"Jeky Chanwala, Isabell Rosenkranz, Peter Kindgren","doi":"10.1016/j.pbi.2025.102830","DOIUrl":"10.1016/j.pbi.2025.102830","url":null,"abstract":"<div><div>Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102830"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145721357","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":"Architects of plant immunity: Structure-informed strategies for engineering plant nucleotide-binding leucine-rich repeat receptors","authors":"Daniel S. Yu, Mark J. Banfield","doi":"10.1016/j.pbi.2025.102828","DOIUrl":"10.1016/j.pbi.2025.102828","url":null,"abstract":"<div><div>Diseases caused by plant pathogens are a major factor decreasing crop yields that lead to food insecurity. To protect against pathogen threats, plants possess a multifaceted immune system that perceive threats derived from plant pathogens, resulting in the activation of immune responses. Evolutionary pressures allow plant pathogens to evolve rapidly and evade recognition by nucleotide-binding leucine-rich repeat (NLR) receptors. In recent years, advancements in our understanding of the molecular and structural basis of effector recognition by NLRs have enabled targeted strategies for engineered receptors that contain novel or expanded recognition profiles. In conjunction with advancements in structural modeling and synthetic biology tools, this has transformed our ability to manipulate plant receptors with precision. Here, we highlight structure-based approaches toward engineering plant NLRs, including integrated domain (ID) engineering and leucine-rich repeat resurfacing, discuss challenges associated with NLR engineering, and highlight future engineering approaches to enhance the plant immune system against pathogen threats.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"89 ","pages":"Article 102828"},"PeriodicalIF":7.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145653702","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 plant epigenome governed by nutrients and metabolism","authors":"Xuerui Nie , Jen Sheen , Ruiqiang Ye","doi":"10.1016/j.pbi.2025.102820","DOIUrl":"10.1016/j.pbi.2025.102820","url":null,"abstract":"<div><div>Nutrients are essential regulators of growth and development across all life forms, serving not only as energetic resources and structural building blocks but also as dynamic signals that govern cell proliferation, metabolism, growth and development. Nutrients and metabolic processes orchestrate plant developmental programs and plasticity via the coordination with dynamic changes in the epigenomic landscape, which is fundamental for governing gene expression programs and developmental transitions in multicellular organisms. In this review, we explore the interplay between nutrition, metabolism, and epigenetic reprogramming in plants, with a particular focus on the novel mechanisms, including nuclear localized metabolic enzymes, moonlighting functions of metabolic enzymes, epigenetic regulators as metabolic sensors, and nutrient sensing and signaling pathways. Elucidating these mechanisms holds significant implications for understanding plant growth and development and improving crop yield and quality.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102820"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145408409","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":"Update on translational control modes in plant cell signaling","authors":"Mauricio A. Reynoso","doi":"10.1016/j.pbi.2025.102799","DOIUrl":"10.1016/j.pbi.2025.102799","url":null,"abstract":"<div><div>Protein synthesis can contribute to plant cell signaling at multiple regulatory levels. Recent studies have expanded the conditions that are directly impacted by translational regulation. This control can balance responses to developmental, environmental, and diverse stress stimuli. Processes with evidence of translational regulation include: immunity to bacterial pathogens, symbiotic interactions, abiotic responses, hormonal perception, light-dependent metabolism, and developmental programs for lateral root initiation, root hair growth, and sepal initiation. Translational control modes rely on the sequence and secondary structure of mRNAs due to the presence of upstream open reading frames (uORFs) and/or internal ribosome entry sites (IRES), protein-binding regions or structures, and the decoding of the epitranscriptomic mRNA modifications such as N<sup>6</sup>-methyladenosine, N<sup>4</sup>-acetylcytidine or pseudouridine. In addition, the post-translational modification of ribosomal proteins and eukaryotic initiation factors such as eIF4G, eIFiso4G, eIF2, as well as changes in ribosome protein composition contribute to translational control. These factors, mRNAs, regulatory proteins and other RNAs can be confined by the formation of biomolecular condensates such as stress granules, processing bodies and others, resulting in paths that modulate translation both globally and specifically. The covered topics place translation as a hub for cell responses during development and within the environmental context. Current understanding of translation has allowed the development of applications in crops, reinforcing the relevance of the study of translational control in plants.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102799"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211711","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":"Monoubiquitination of histone H2A and H2B: News and views","authors":"Sara Farrona , Fredy Barneche","doi":"10.1016/j.pbi.2025.102824","DOIUrl":"10.1016/j.pbi.2025.102824","url":null,"abstract":"<div><div>Fine-tuning eukaryotic gene expression heavily relies on chromatin regulatory mechanisms involving dynamic exchanges and modifications of histones. Here, we review the main pathways that mediate histone H2A and H2B monoubiquitination and deubiquitination in <em>Arabidopsis thaliana</em>. These histone post-translational modifications are linked to multiple chromatin regulatory layers, enabling distinct functional outcomes across the genome and in response to developmental and environmental signals. Indeed, while H2A deubiquitination primarily attenuates transcription either independently or together with PRC2-mediated H3K27 trimethylation, H2B monoubiquitination facilitates nucleosome dynamics and RNA polymerase II progression during gene activation. Given the widespread role of histone deubiquitination mechanisms in plant development, we also discuss how H2Aub and H2Bub homeostasis influences genome regulation. Finally, by referencing yeast and metazoans, we highlight examples of distinctive plant molecular mechanisms and epigenetic interplays involving histone ubiquitination.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102824"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145470864","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 cellular epigenetic blueprint of plant regeneration","authors":"Yiting He , Lin Xu , Qikun Liu","doi":"10.1016/j.pbi.2025.102784","DOIUrl":"10.1016/j.pbi.2025.102784","url":null,"abstract":"<div><div>Plants exhibit remarkable regenerative capacities, enabling tissue repair, <em>de novo</em> organogenesis, and somatic embryogenesis in response to mechanical injury or phytohormone induction. At the cellular level, this process is driven by the establishment of pluripotency and cell fate specification, regulated through dynamic epigenomic remodeling. Emerging studies have begun to unravel the intricate regulatory circuits governing regeneration in a cell-type- and lineage-specific manner. In this short review, we synthesize key findings from interconnected studies, exploring potential common mechanisms underlying the epigenetic regulation of plant regeneration. We also highlight promising research directions, emerging tools, and innovative strategies to investigate plant regeneration epigenetics at single-cell and single-cell-type resolution. These technological advances will provide critical insights into plant cell fate determination, the fundamental process governing regeneration.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102784"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933479","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}
Suxin Xiao, Lingxiao Luo, Minqi Yang, Hang He, Yue Zhou
{"title":"Fine-scale 3D chromatin architectures and their regulatory mechanisms in plants","authors":"Suxin Xiao, Lingxiao Luo, Minqi Yang, Hang He, Yue Zhou","doi":"10.1016/j.pbi.2025.102786","DOIUrl":"10.1016/j.pbi.2025.102786","url":null,"abstract":"<div><div>Recent studies have demonstrated that fine-scale chromatin architectures, including topologically associating domains (TADs) and chromatin loops, play critical roles in plant growth and development. Advanced technologies with increased resolution and reduced sequencing costs have provided more detailed interaction information, enabling the identification of additional chromatin loops and their associated biological processes. In this review, we present a comprehensive overview of the technologies that have been successfully applied in plants, followed by a detailed description of KNOT, fountain, TAD and chromatin loop. At the same time, some regulators associated with three-dimensional (3D) chromatin architectures are also discussed to understand the regulation of 3D chromatin architecture in plants. Furthermore, this review offers directions of 3D chromatin architecture in plants in terms of both technological developments and scientific mechanisms.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102786"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145061054","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":"Engineering chromatin and transcriptome regulation in plants: Strategies, challenges, and outlook","authors":"Jason Gardiner","doi":"10.1016/j.pbi.2025.102810","DOIUrl":"10.1016/j.pbi.2025.102810","url":null,"abstract":"<div><div>In plants, altering the accessibility to DNA through chromatin modification is a key component of transcriptome regulation, crucial for normal development and environmental response. In recent years, our understanding of how and why plants engineer their chromatin has greatly improved, leading to strategies that now enable us to engineer chromatin through both targeted and non-targeted approaches. Although new and improved systems for chromatin engineering are continually emerging, it is evident that developing a diverse toolbox of strategies to tackle various unique challenges is necessary. This review outlines different methods for non-targeted and targeted chromatin engineering, enabling the manipulation of the transcriptome through chromatin engineering. It also discusses particular challenges in the field of chromatin engineering in plants and offers a brief outlook on potential future directions.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102810"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145262907","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}