New Phytologist最新文献

{"title":"Spray‐induced gene silencing boosts functional genomics in symbiotic fungi","authors":"Ramesh Raju Vetukuri, Luisa Lanfranco, Katie Stevens","doi":"10.1111/nph.70269","DOIUrl":"https://doi.org/10.1111/nph.70269","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"166 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144165277","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":"BBX32 integrates ethylene and light signaling to delay apical hook opening and optimize seedling soil emergence","authors":"Nevedha Ravindran, Kavuri Venkateswara Rao, Sourav Datta","doi":"10.1111/nph.70236","DOIUrl":"https://doi.org/10.1111/nph.70236","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>In terrestrial plants, seeds often germinate and initiate early development in the darkness under layers of soil. Soil overlay promotes ethylene accumulation to maintain the hook until the seedlings reach the soil surface. During this phase of etiolated growth and soil emergence, seedlings perceive changing light fluence. Coordinated interplay of the ethylene and light signaling pathways ensures optimal timing of apical hook opening and enhanced emergence.</li>\u0000<li>Here, we report that ethylene and light cooperatively act on the B-box protein BBX32 to regulate apical hook opening and enhance soil emergence<i>.</i> Ethylene induces expression and accumulation of BBX32 in the apical hook in the dark. CONSTITUTIVE PHOTOMORPHOGENIC 1 degrades BBX32 in the dark while light enhances <i>BBX32</i> expression and accumulation in the apical hook during de-etiolation. <i>bbx32</i> mutants exhibit accelerated apical hook opening, while <i>BBX32</i> overexpressing lines show delayed opening.</li>\u0000<li>Genetic analyses reveal that BBX32 functions in concert with PHYTOCHROME-INTERACTING FACTOR 3 to negatively regulate apical hook opening during de-etiolation. BBX32 enhances <i>HOOKLESS 1</i> expression in a PIF3-dependent manner to delay hook opening. Under soil cover, <i>bbx32</i> and <i>35S:BBX32</i> seedlings exhibit reduced and enhanced seedling emergence, respectively.</li>\u0000<li>Our study illustrates the role of BBX32 in synchronizing light and ethylene-mediated apical hook opening and seedling emergence.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"18 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154199","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":"PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization","authors":"Xue‐Chan Tian, Shuai Nie, Douglas Domingues, Alexandre Rossi Paschoal, Li‐Bo Jiang, Jian‐Feng Mao","doi":"10.1111/nph.70211","DOIUrl":"https://doi.org/10.1111/nph.70211","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models.</jats:list-item> <jats:list-item>Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features – ORF coverage, complex Fourier average, and atomic Fourier amplitude – that effectively distinguish lncRNAs from mRNAs.</jats:list-item> <jats:list-item>We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species.</jats:list-item> <jats:list-item>PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://github.com/xuechantian/PlantLncBoost\">https://github.com/xuechantian/PlantLncBoost</jats:ext-link>) and has been integrated into a comprehensive analysis pipeline, Plant‐LncRNA‐pipeline v.2 (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://github.com/xuechantian/Plant-LncRNA-pipeline-v2\">https://github.com/xuechantian/Plant‐LncRNA‐pipeline‐v2</jats:ext-link>).</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"35 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153640","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":"An isoflavone reductase-like protein MtIFL negatively regulates nodule symbiosis in Medicago truncatula","authors":"Yongrui Shen, Yan Yan, Ting Yin, Hongyu Zhang, Haijing Zhu, Siyu Zhang, Haiqing Hu, Gehong Wei, Minxia Chou","doi":"10.1111/nph.70251","DOIUrl":"https://doi.org/10.1111/nph.70251","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Flavonoids are valuable metabolites produced by legumes, including <i>Medicago truncatula</i>, and play crucial roles in signaling communication during legume–<i>rhizobium</i> symbiosis. Isoflavone reductase proteins (IFRs) are involved in the biosynthesis of isoflavones and plant defense regulation. However, their role in symbiotic nitrogen fixation remains mostly elusive.</li>\u0000<li>Here, 13 putative <i>IFR</i> gene family members were identified, and an <i>IFR</i>-like gene named <i>MtIFL</i> was functionally characterized through expression patterns, phenotypic characterizations, flavonoid metabolome, and transcriptome analyses. Furthermore, the binding partner of <i>MtIFL</i> was investigated using Y1H, EMSA, and Dual-LUC assays.</li>\u0000<li><i>MtIFL</i> was strongly induced in the process of nodule development and expressed in the meristem and infection zone of mature nodules. Knockout of <i>MtIFL</i> promoted nodulation, while overexpression of <i>MtIFL</i> induced premature senescence of nodules. Further investigations revealed that <i>MtIFL</i> negatively regulates nitrogen-fixing symbiosis by mediating isoflavone metabolism, and MtNIN regulates <i>MtIFL</i> expression by binding to the hNRE motif.</li>\u0000<li>Overall, our findings suggest that <i>MtIFL</i> negatively regulates nodule formation, thereby influencing the survival of rhizobia in nodule cells. MtNIN regulates <i>MtIFL</i> expression and may play a role in isoflavone metabolism. These results provide novel insights into the function of IFRs in symbiotic nodulation and the role of flavonoids in nodule development.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"26 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154319","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":"Shining a new light on parasitic plants: resistance to invasion","authors":"Alex Fajardo, Claudia Reyes‐Bahamonde, Francisco E. Fontúrbel, Frida I. Piper, Ragan M. Callaway","doi":"10.1111/nph.70203","DOIUrl":"https://doi.org/10.1111/nph.70203","url":null,"abstract":"SummaryParasitic plants, those that directly acquire resources from other plants, are distributed across all biomes on earth. They can be restricted to a single host, or they can be generalists, but with preferences. <jats:italic>Tristerix corymbosus</jats:italic> (Loranthaceae) is a native generalist hemiparasite in Chile but infests many nonnative tree species and appears to suppress them more than its native hosts, indicating its potential to provide substantial ecological resistance. These patterns suggest the novel phenomenon of native hemiparasite host switching from slow‐growing native hosts to fast‐growing nonnatives, which may provide substantial biotic resistance to invasion, but they also have fascinating ecological, physiological, and evolutionary implications. For example, resistance to invasion contrasts with traditional views of parasitic plants as forest plagues. Instead, <jats:italic>Tristerix</jats:italic> may function in invaded forests as a keystone species with negative direct effects on invaders and positive indirect interactions with natives. The negative effects of <jats:italic>Tristerix</jats:italic> on nonnative species provide a more complete understanding of the various roles native parasitic plants can have in resistance to invasion.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"145 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153639","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":"Uncovering the reciprocal effects of plant polyploidy and the microbiome: implications for understanding of polyploid success","authors":"Tia‐Lynn Ashman","doi":"10.1111/nph.70226","DOIUrl":"https://doi.org/10.1111/nph.70226","url":null,"abstract":"SummaryPolyploidy plays a major role in diversification and speciation of almost all plants. Separately, the microbiome is recognized for its ubiquitous role in plant functioning. Despite the importance of both processes, we lack a synthetic picture of their reciprocal relationship. I forge this missing linkage by presenting the ways in which plant polyploidy can shape the microbiome and how the microbiome in turn can affect polyploid phenotype and fitness. I illustrate these interactions by drawing on the small, but compelling, set of comparisons of the plant–microbial community interaction with taxa representing different stages of the polyploid continuum and thereby shed light on how the advantages of polyploidy may be influenced by microbes. I use findings from a range of studies to build the case for plant–microbiome reciprocal interactions in both key pathways for polyploid persistence: overcoming their minority cytotype disadvantage and increasing competitive ability and/or niche shifts relative to diploids. I put forward how the microbiome likely plays a role in polyploid stress tolerance, abiotic niche breadth, range limits and coexistence. I conclude by identifying the research needed to test these hypotheses and how doing so could transform our understanding of polyploidy as a driver of plant ecology and evolution.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"51 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153636","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":"Signaling defenses with color: a meta-analysis of leaf color variation, palatability, and herbivore damage","authors":"Tatiana Cornelissen, Fernando A. O. Silveira, Susan Vieira Gomes, Xosé Lopez-Goldar, Sylvie Martin-Eberhardt, William Wetzel","doi":"10.1111/nph.70243","DOIUrl":"https://doi.org/10.1111/nph.70243","url":null,"abstract":"&lt;h2&gt; Introduction&lt;/h2&gt;\u0000&lt;p&gt;A complex interplay of leaf functional traits such as size (Zhu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;), specific leaf area (Poorter &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2004&lt;/span&gt;; Kozlov &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;), shape (Ferris, &lt;span&gt;2019&lt;/span&gt;; Higuchi &amp; Kawakita, &lt;span&gt;2019&lt;/span&gt;), nutrient stoichiometry (Njovu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;; Schön &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;), and mechanical and chemical defenses (Hanley &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2007&lt;/span&gt;; Caldwell &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2016&lt;/span&gt;; Agrawal &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2021&lt;/span&gt;) determines how herbivores find and use resources. Leaf palatability, therefore, reflects a syndrome of coordinated leaf traits that ultimately shape plant resistance and/or tolerance to insect herbivory, which in turn is countered by insect adaptation, driving the coevolutionary dynamics between insects and host plants (Ehrlich &amp; Raven, &lt;span&gt;1964&lt;/span&gt;; Archetti &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2009&lt;/span&gt;; Agrawal &amp; Zhang, &lt;span&gt;2021&lt;/span&gt;). Despite overwhelming evidence of the effects of plant interspecific trait variability on herbivory (see Wetzel &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;; Liu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;; Zvereva &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;), considerably little attention has been paid to intraspecific leaf color variability that occurs between plant populations or within individual plants. The intraspecific diversity in leaf size, shape, morphology, and color is typically suggested as the product of selective pressures optimizing trait combinations to cope with abiotic conditions that drive strategies of resource use, acquisition, and conservation (Campitelli &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2008&lt;/span&gt;; Hughes &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2022&lt;/span&gt;). However, leaf functional traits also influence how plants interact with insect herbivores, but which leaf traits influence variation in herbivory and how these variations arise and are selected have been a long-lasting debate in plant–herbivore interactions (Harper, &lt;span&gt;1977&lt;/span&gt;; Carmona &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2011&lt;/span&gt;; Muiruri &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;).&lt;/p&gt;\u0000&lt;p&gt;While the role of color has been extensively studied in animals, particularly in the contexts of color vision, aposematism, and sexual selection (see Wiens &amp; Emberts, &lt;span&gt;2024&lt;/span&gt;), a comprehensive understanding from the plant perspective is emerging more recently (but see Landi &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;; Renoult &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;). Research has predominantly focused on flower and fruit color, a key trait mediating interactions with pollinators, frugivores, and seed dispersers. However, the significance of leaf color and its implications for understanding plant–herbivore interactions and plant defense mechanisms remain largely underexplored. Leaf color variability is commonly observed in phylogenetically unrelated species and across biogeographic regions (e.g. Lee &amp; Collins, &lt;span&gt;2001&lt;/span&gt;; Lee, &lt;span&gt;2002&lt;/span&gt;; Gong &lt;i&gt;","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"503 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154200","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":"Ecosystem consequences of functional diversity in forests and implications for restoration.","authors":"Chen Chen,Franca J Bongers,Bernhard Schmid,Keping Ma,Xiaojuan Liu","doi":"10.1111/nph.70247","DOIUrl":"https://doi.org/10.1111/nph.70247","url":null,"abstract":"Global forest restoration initiatives provide an important chance to recover biodiversity and enhance forest functions and services. Over recent decades, functional diversity (FD) has been regarded as a key driver of the positive relationships between biodiversity and ecosystem functioning (BEF). Despite extensive observations on the associations between tree FD and various forest ecosystem functions, we still lack a sufficient mechanistic understanding of the ecosystem consequences of FD in forests to provide scientific guidance for global restoration efforts. Hereafter, we revisit and seek to clarify the various pathways through which tree FD influences forest productivity, for example, species complementarity and dominance effects. We discuss how tree FD affects ecosystem functions via changes in other trophic levels, for example, through providing more or more diverse food, habitat, or litter. Future work on forest BEF relationships should examine the dependence of FD effects on environmental context and predict FD effects under environmental change scenarios. Ultimately, we propose several strategies for incorporating FD into forest restoration designs to reinstate BEF under current and future environmental conditions.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"82 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136774","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":"Correction to 'Quantifying the production of plant pollen at the farm scale'.","authors":"","doi":"10.1111/nph.70204","DOIUrl":"https://doi.org/10.1111/nph.70204","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"64 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136772","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":"Mutational load and adaptive variation are shaped by climate and species range dynamics in Vitis arizonica.","authors":"Christopher J Fiscus,Jonás A Aguirre-Liguori,Garren R J Gaut,Brandon S Gaut","doi":"10.1111/nph.70238","DOIUrl":"https://doi.org/10.1111/nph.70238","url":null,"abstract":"Genetic load can reduce fitness and hinder adaptation. While its genetic underpinnings are well established, the influence of environmental variation on genetic load is less well characterized, as is the relationship between genetic load and putatively adaptive genetic variation. This study examines the interplay among climate, species range dynamics, adaptive variation, and mutational load - a genomic measure of genetic load - in Vitis arizonica, a wild grape native to the American Southwest. We estimated mutational load and identified climate-associated adaptive genetic variants in 162 individuals across the species' range. Using a random forest model, we analyzed the relationship between mutational load, climate, and range shifts. Our findings linked mutational load to climatic variation, historical dispersion, and heterozygosity. Populations at the leading edge of range expansion harbored higher load and fewer putatively adaptive alleles associated with climate. Climate projections suggest that V. arizonica will expand its range by the end of the century, accompanied by a slight increase in mutational load at the population level. This study advances understanding of how environmental and geographic factors shape genetic load and adaptation, highlighting the need to integrate deleterious variation into broader models of species response to climate change.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"44 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136773","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}