Nature Plants最新文献

{"title":"Transcription factor binding divergence drives transcriptional and phenotypic variation in maize","authors":"Mary Galli, Zongliang Chen, Tara Ghandour, Amina Chaudhry, Jason Gregory, Fan Feng, Miaomiao Li, Nathaniel Schleif, Xuan Zhang, Yinxin Dong, Gaoyuan Song, Justin W. Walley, George Chuck, Clinton Whipple, Heidi F. Kaeppler, Shao-shan Carol Huang, Andrea Gallavotti","doi":"10.1038/s41477-025-02007-8","DOIUrl":"https://doi.org/10.1038/s41477-025-02007-8","url":null,"abstract":"<p>Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as <i>Vgt1</i>, an important determinant of flowering time, and <i>DICE</i>, an herbivore resistance enhancer. CRISPR–Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"90 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144269169","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":"Identifying hotspots of naturally regenerating forests","authors":"Catherine Walker","doi":"10.1038/s41477-025-02037-2","DOIUrl":"https://doi.org/10.1038/s41477-025-02037-2","url":null,"abstract":"<p>Using remotely sensed forest cover data spanning from 1990 to 2023, researchers at the University of Cambridge, Christopher Bousfield and David Edwards, mapped the spatial distribution and ages of regenerating tropical moist forests. This study, published in <i>Nature Ecology &amp; Evolution</i>, revealed that five countries account for 52% of the 51 million hectares of regenerating tropical moist forests — Brazil, Indonesia, the Democratic Republic of Congo, Colombia and Myanmar. Just 6% of these regenerating forests are over 20 years old, primarily located in the Americas, whereas more than half are less than 5 years old, which suggests that deforested landscapes are caught in a cycle of farm abandonment, regeneration, deforestation and agricultural production.</p><p>A random forest model incorporating factors related to environmental, geographic and anthropogenic factors revealed that landscape forest characteristics were the best predictors of regenerating forest age. Older regenerating forests were more likely to be found in regions of high forest cover and connectivity, further supporting the need to protect old-growth forests to prevent clearance of regenerating forests.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"558 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144252763","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":"TIR immune signalling is blocked by phosphorylation to maintain plant growth","authors":"Jun Li, Sisi Chen, Bo Yu, Qingzhong Li, Ruijia Liu, Zaiqing Wang, Li Wan, Yang Zhao","doi":"10.1038/s41477-025-02012-x","DOIUrl":"https://doi.org/10.1038/s41477-025-02012-x","url":null,"abstract":"<p>Toll/interleukin-1 receptor (TIR) domain proteins are immune signalling components and function as NAD⁺-cleaving enzymes to activate defence responses. In plants, TIR activation triggers cell death and severely represses growth, especially under osmotic stress, while in animals, it promotes axon degeneration. However, the mechanisms regulating TIR suppression remain unclear. Here we show that TIR NADase activity requires a conserved serine residue spatially close to the catalytic glutamate. The osmotic-stress-activated plant Ca²⁺-dependent protein kinases (CPKs), the mammalian Ca²⁺/calmodulin-dependent protein kinase II delta (CAMK2D) and TANK-binding kinase 1 (TBK1) phosphorylate TIR domains at this conserved serine, which blocks TIR NADase activities and functions, thereby maintaining growth in plants and suppressing SARM1 TIR signalling in animals. Our findings define a fundamental molecular mechanism by which phosphorylation at a conserved serine residue inhibits TIR signalling in plants and animals and sustains plant growth.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"6 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144238242","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 conserved cytochrome for organ development","authors":"Raphael Trösch","doi":"10.1038/s41477-025-02031-8","DOIUrl":"https://doi.org/10.1038/s41477-025-02031-8","url":null,"abstract":"<p>The <i>Arabidopsis</i> genome encodes 15 cytochrome b5 proteins, most of which have metabolic functions such as nitrate reduction or sphingolipid desaturation. Of these cytochrome b5 proteins, only RLF is reported to be required for organ development. Specifically, <i>rlf</i> mutants display defective lateral root formation as well as reduced primary root growth and smaller leaf size. In these mutants, auxin signalling is unaffected, suggesting that the role of RLF in organ development is independent of auxin signalling. Cytochrome b5 proteins have a haem-binding domain and coordinated haem is required for their electron carrier function. However, it is not clear whether haem binding and thus the canonical electron carrier function are required for RLF’s role in organ development, and whether this role is conserved in plants.</p><p>The researchers confirmed in vitro haem binding to purified <i>Arabidopsis</i> RLF spectroscopically by the presence of the typical Soret and α/β bands. Two conserved histidine residues were identified, which are required for in vitro haem binding. The lateral root phenotype of <i>rlf</i> mutants could be complemented with wild-type RLF but not when either of the two histidine residues were mutated to alanine, suggesting that haem binding is also required for the in planta functionality of RLF. Phylogenetic analysis showed that RLF orthologues form a separate clade among cytochrome b5 proteins that is conserved in plants. The wild-type RLF from <i>M. polymorpha</i> was confirmed to bind haem in vitro, and MpRLF could fully complement the lateral root phenotype of <i>Arabidopsis rlf</i> mutants, suggesting functional conservation. In <i>Marchantia</i>, RLF is expressed both in vegetative and reproductive growth phases, and mutants display stunted growth and various defects in the development of organs with both vegetative and reproductive functions. These phenotypes can be partially complemented by the <i>Arabidopsis</i> RLF orthologue, again showing considerable functional conservation. Transcriptomics showed that predominantly genes with metabolic functions were differentially expressed between <i>rlf</i> mutants and the wild type, including genes involved in nitrate metabolism, which is known to affect lateral root formation. This might suggest that RLF affects organ development through a metabolic function; it would be interesting to confirm such a hypothesis by finding direct interactors of RLF in future.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"1 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144238241","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":"Leaf venation network evolution across clades and scales","authors":"Ilaine Silveira Matos, Bradley Vu, Joseph Mann, Emily Xie, Srinivasan Madhavan, Satvik Sharma, Izzi Niewiadomski, Andrea Echevarria, Connor Tomaka, Sonoma Carlos, Monica Antonio, Ashley Chu, Meg Scudder, Nicole Yokota, Hailey J. Park, Natalie Vuong, Mickey Boakye, Miguel A. Duarte, Caroline Pechuzal, Luiza Maria T. Aparecido, Mia B. Franco, Ryan Jen Wong, Jocelyn Liu, Emily Guevara Heredia, Brad Boyle, Martha Ryan, Rafael E. Cárdenas, Brian J. Enquist, Diane M. Erwin, Holly Forbes, Kyle Dexter, Mark Fricker, Benjamin W. Blonder","doi":"10.1038/s41477-025-02011-y","DOIUrl":"https://doi.org/10.1038/s41477-025-02011-y","url":null,"abstract":"<p>Leaf venation architecture varies greatly among living and fossil plants. However, we still have a limited understanding of when, why and in which clades new architectures arose and how they impacted leaf functioning. Using data from 1,000 extant and extinct (fossil) plants, we reconstructed approximately 400 million years of venation evolution across clades and vein sizes. Overall, venation networks evolved from having fewer veins and less smooth loops to having more veins and smoother loops, but these changes only occurred in small and medium vein sizes. The diversity of architectural designs increased biphasically, first peaking in the Paleozoic, then decreasing during the Cretaceous, then increasing again in the Cenozoic, when recent angiosperm lineages initiated a second and ongoing phase of diversification. Vein evolution was not associated with temperature and CO₂ fluctuations but was associated with insect diversification. Our results highlight the complexity of the evolutionary trajectory and potential drivers of venation network architecture.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"18 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144228846","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":"Ordovician marine Charophyceae fossils provide insights into land plant evolution","authors":"","doi":"10.1038/s41477-025-02010-z","DOIUrl":"https://doi.org/10.1038/s41477-025-02010-z","url":null,"abstract":"Our discovery of fossil charophycean algae much older than any previously reported confirms that some key morphological innovations associated with the evolutionary transition between streptophyte algae and land plants had already occurred around 453 million years ago. These fossils support derivation of land plants from streptophyte algae during the Ordovician period.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"8 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144202170","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":"The late rise of sky-island vegetation in the European Alps","authors":"Lara M. Wootton, Florian C. Boucher, Charles Pouchon, Cristina Roquet, Eric Coissac, Julien Renaud, Inger G. Alsos, Pierre G. Valla, Laurent Husson, Matthias Bernet, Christophe Perrier, Rolland Douzet, Maxime Rome, Jean-Gabriel Valay, Adriana Alberti, France Denoeud, Niklaus E. Zimmermann, Patrick Wincker, Wilfried Thuiller, Sébastien Lavergne","doi":"10.1038/s41477-025-02001-0","DOIUrl":"https://doi.org/10.1038/s41477-025-02001-0","url":null,"abstract":"<p>Our understanding of the emergence of mountain floras rests on our ability to infer how orogeny, landscape dynamics and climate change altered their evolutionary trajectories. Here we reconstruct the assembly of the diverse sky-island flora of the European Alps and test the impact of key geo-climatic events. We use a dated 5,231-species phylogeny, including 96% of the sky-island flora. The assembly of this flora occurred through the colonization of over a thousand distinct lineages, of which 46% speciated from their lowland or non-Alpine ancestor and 6% underwent in situ cladogenesis. The young ages of extant sky-island lineages show that their accumulation was decoupled from ancient geo-climatic events but accelerated throughout the Plio-Pleistocene. The sky-island vegetation therefore assembled through recent lineage turnover, which was triggered, rather than impeded, by Pleistocene glacial intensification. This perspective challenges previous assumptions and highlights the complex interplay of geo-climatic factors in shaping the intricate tapestry of alpine floras.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"98 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144193033","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":"Ordovician marine Charophyceae and insights into land plant derivations","authors":"Lijing Liu, Jian Han, Zhifei Zhang, Qing Tang, Ke Pang, Ruiyun Li, Yasheng Wu, Hong Hua, Bin Guo, Chunfang Cai, Robert Riding","doi":"10.1038/s41477-025-02003-y","DOIUrl":"https://doi.org/10.1038/s41477-025-02003-y","url":null,"abstract":"<p>The emergence of land plants was a pivotal development in Earth history. It has been postulated that the evolutionary transition from freshwater streptophyte algae to land plants, or the canalization of plant meiosis, was completed during the Middle Ordovician (~460 Ma). However, the absence of undisputed streptophyte algal fossils (for example, Charophyceae) earlier than the late Silurian (~425 Ma) has obscured this link between streptophyte algae and land plants. Here we describe a marine Charophyceae fossil, <i>Tarimochara miraclensis</i> gen. et sp. nov., from early and middle Katian (Late Ordovician, ~453–449 Ma) marine limestones in northwestern China. This discovery demonstrates that at least some species of Charophyceae inhabited shallow normal marine environments at that time. Moreover, these early Charophyceae show that some key morphological innovations associated with an evolutionary transition between streptophyte algae and land plants had occurred before the early Katian. This provides crucial evidence relevant to the origins of land plants.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"3 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144176810","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":"Rethinking field trials","authors":"","doi":"10.1038/s41477-025-02016-7","DOIUrl":"https://doi.org/10.1038/s41477-025-02016-7","url":null,"abstract":"Field trials are indispensable for the application of agronomic genes. However, whether a scientific publication needs to include data on field trials is a very complicated issue.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"4 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123048","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":"How vacuolar sugar transporters evolve and control cellular sugar homeostasis, organ development and crop yield","authors":"Lingcheng Zhu, Jincheng Lan, Tao Zhao, Mingjun Li, Yong-Ling Ruan","doi":"10.1038/s41477-025-02009-6","DOIUrl":"https://doi.org/10.1038/s41477-025-02009-6","url":null,"abstract":"<p>Sugar exchange among different subcellular compartments is central for achieving cellular sugar homeostasis and directly affects the yield and quality of many horticultural and field crops. While a portion of photosynthesis-originated sugars is metabolized through glycolysis upon entering the cytosol, the remainder is reversibly channelled to the vacuole, mediated by different families of vacuolar sugar transporter (VST) located on the vacuolar membrane, the tonoplast. Historically, sugar transporters operating on plasma membranes have been studied more than those on tonoplasts. Recently, however, several breakthroughs have shed light on (1) the distinct roles of VSTs in plant development and stress responses and (2) how seemingly unrelated classes of VSTs act together to modulate sugar influx into and efflux from the vacuoles. Here we evaluate these advances, analyse the evolution of VSTs and identify knowledge gaps and future directions for better understanding and manipulation of cytosolic–vacuolar sugar exchange to optimize plant performance.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"45 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104737","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}