New Phytologist最新文献

{"title":"COmapper: high‐resolution mapping of meiotic crossovers by long‐read sequencing in Arabidopsis","authors":"Dohwan Byun, Namil Son, Heejin Kim, Jaeil Kim, Jihye Park, Sang‐jun Park, Hyein Kim, Jaebeom Kim, Juhyun Kim, Seula Lee, Youbong Hyun, Piotr A. Ziolkowski, Ian R. Henderson, Kyuha Choi","doi":"10.1111/nph.70304","DOIUrl":"https://doi.org/10.1111/nph.70304","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Meiotic crossovers rearrange existing genetic variation between homologous chromosomes, profoundly affecting genomic diversity. Crossovers are typically constrained to one to three events per chromosome pair, and their distribution is shaped by chromatin accessibility and DNA polymorphisms. Genome‐wide crossover maps can be generated in plants by high‐throughput short‐read sequencing or linked‐read sequencing.</jats:list-item> <jats:list-item>Here, we use long‐read nanopore sequencing technology to develop a crossover mapping pipeline, COmapper, for high‐resolution mapping of genome‐wide crossovers from pooled DNA of F<jats:sub>1</jats:sub> hybrid pollen and F<jats:sub>2</jats:sub> recombinant seedlings derived from a cross between <jats:italic>Arabidopsis thaliana</jats:italic> accessions Col and L<jats:italic>er</jats:italic>. We validate the high accuracy of COmapper by applying nanopore long‐read sequencing to the pooled DNA of <jats:italic>Arabidopsis</jats:italic> F<jats:sub>2</jats:sub> individuals with crossovers mapped by short‐read sequencing.</jats:list-item> <jats:list-item>Using the COmapper, we constructed high‐resolution genomic maps of crossovers using F<jats:sub>1</jats:sub> hybrid pollen and F<jats:sub>2</jats:sub> seedlings in wild‐type (WT) and crossover‐elevated <jats:italic>recq4a recq4b</jats:italic> mutants, showing results comparable to short‐read sequencing. Crossovers were enriched at gene‐proximal promoters in WT and increased but reshaped by high polymorphism density in <jats:italic>recq4a recq4b</jats:italic>.</jats:list-item> <jats:list-item>We propose that COmapper will be widely applicable for exploring the effects of genetic, epigenetic, and environmental changes on the crossover patterns across diverse plant species.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"12 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144319845","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 collector practices that shape spatial, temporal, and taxonomic bias in herbaria.","authors":"Ryan J Schmidt,Kristen E Saban,Lena Struwe,Charles C Davis","doi":"10.1111/nph.70297","DOIUrl":"https://doi.org/10.1111/nph.70297","url":null,"abstract":"Natural history collections (NHCs) are essential for studying biodiversity. Although spatial, temporal, and taxonomic biases in NHCs affect analyses, the influence of collector practices on biases remains largely unexplored. We utilized one million digitized specimens collected in the northeastern United States by c. 10 000 collectors to investigate how collector practices shape spatial, temporal, and taxonomic biases in NHCs; and similarities and differences between practices of more- and less-prolific collectors. We identified six common collector practices, or collection norms: collectors generally collected different species, from multiple locations, from sites sampled by others, during the principal growing season, species identifiable outside peak collecting months, and species from species-poor families and genera. Some norms changed over decades, with different taxa favored during different periods. Collection norms have increased taxonomic coverage in NHCs; however, collectors typically avoided large, taxonomically complex groups, causing their underrepresentation in NHCs. Less-prolific collectors greatly enhanced coverage by collecting during more months and from less-sampled locations. We assert that overall collection biases are shaped by shared predictable collection norms rather than random practices of individual collectors. Predictable biases offer an opportunity to more effectively address biases in future biodiversity models.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"98 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328686","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 increasingly powerful term mycorrhiza warrants attention.","authors":"Paola Bonfante,Andrea Genre","doi":"10.1111/nph.70324","DOIUrl":"https://doi.org/10.1111/nph.70324","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"16 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320351","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 PHYTOCHROME INTERACTING FACTOR 3, a bHLH transcription factor, promotes thermosensory growth by directly activating PIF4 transcription and its protein accumulation in Arabidopsis.","authors":"Sreya Das,Annayasa Modak,Mohan Singh Rajkumar,Vikas Garhwal,Vishmita Sethi,Mukesh Jain,Sreeramaiah N Gangappa","doi":"10.1111/nph.70278","DOIUrl":"https://doi.org/10.1111/nph.70278","url":null,"abstract":"The role of PHYTOCHROME INTERACTING FACTOR 3 (PIF3) in thermomorphogenesis, despite being a crucial regulator of photosensory hypocotyl growth in Arabidopsis, remains unknown. Here, we demonstrate PIF3 as a key and novel component of the thermosensory pathway. pif3 mutants show reduced sensitivity to warm temperature-induced hypocotyl elongation, which is more pronounced at higher light intensities. pif3 mutant exhibits moderate impairment in petiole elongation and flowering. By contrast, PIF3 overexpression lines show constitutive thermomorphogenic responses. Whole-genome transcriptome analysis revealed that genes induced by warm temperature are significantly downregulated in the pif3 mutant but are constitutively upregulated in the PIF3 overexpression line. Moreover, PIF3 directly activates PIF4 transcription by binding to the PIF-binding element (PBE-box) in a temperature-dependent manner. Chromatin immunoprecipitation (ChIP) and biochemical data indicate that PIF4 binding to its target genes requires PIF3. The physical interaction between PIF3 and PIF4 is likely required for the optimal expression of downstream genes involved in metabolism and growth. Epistatic and gene regulation analysis further revealed that PIF3 functions in PIF4-dependent and PIF4-independent pathways to regulate gene expression. This study unravels the novel role, and mechanism through which, PIF3 promotes thermomorphogenic growth in Arabidopsis.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"15 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320026","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":"Fruit nectar or prefruit nectar? Implication of the postfloral nectar of Dendrobium chrysotoxum (Orchidaceae).","authors":"Zongmin Mou,Fan Xiao,Wen Yang,Ding Dong,Enda Sun,Zhengping Yao,Bo Long,Dake Zhao","doi":"10.1111/nph.70318","DOIUrl":"https://doi.org/10.1111/nph.70318","url":null,"abstract":"Postfloral nectar presenting on reproductive organs after pollination generally functions in plant defense to protect fruits and seeds, but the mechanisms for postfloral nectary development and nectar secretion remain largely unknown. We report the first case of postfloral nectar production in the genus Dendrobium (Orchidaceae). D. chrysotoxum produced postfloral nectar on the surface of the inferior ovary after pistil pollination. The features of postfloral nectar secretion were revealed through anatomical and histochemical approaches, transcriptome and metabolome analysis, pollination experiments, and field observations. A key role of stigmatic pollen germination in postfloral nectar induction was demonstrated as well as the ant attraction effect of the postfloral nectar. Unexpectedly, the secretion of postfloral nectar ceased before ovule fertilization, making it more like 'prefruit nectar' than 'fruit nectar' (generally referred to the postfloral nectar occurring on organs that used to be floral ovaries) since the ovaries had not yet become fruits. The clarification of pollen germination in postfloral nectar induction and the provoking thought to define postfloral nectar based on the fertilization status provide new insights into the understanding of postfloral nectar.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"44 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320224","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":"Old player, new roles: defining the role of the plastidial phosphorylase.","authors":"David Seung,Slawomir Orzechowski,Joerg Fettke","doi":"10.1111/nph.70308","DOIUrl":"https://doi.org/10.1111/nph.70308","url":null,"abstract":"The plastidial phosphorylase (Pho1 or Phs1; E.C. 2.4.1.1) is a ubiquitous enzyme among plants that catalyzes the formation and degradation of glucans. Although the first report connecting Pho1 with starch metabolism came out > 80 years ago, its precise role is still a matter of debate. In this article, we evaluate the catalytic and regulatory mechanisms of Pho1 in the context of known mechanisms in its animal, fungal, and bacteria homologs. We further discuss recent breakthroughs in understanding Pho1's function in initiating starch granule formation. This role is relevant to both photosynthetic and nonphotosynthetic tissues, as loss of Pho1 affects the regulation of the number of transitory starch granules in Arabidopsis leaves under various metabolic contexts, as well as the number of storage starch granules and/or starch granule morphology in wheat endosperm and potato tubers. Our comparison of phosphorylases across kingdoms reveals several regulatory mechanisms that require further investigation in plants. We also discuss emerging research on Pho1 protein interactions that give rise to other metabolic processes, such as photosynthesis. Overall, these multiple emerging roles of phosphorylase emphasize its importance in plant metabolism and its broad potential as a target for crop improvement.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"1 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144311590","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":"Detecting the enemy or being manipulated by your attacker? Herbivore-derived elicitors of plant responses: an introduction to a Virtual Issue","authors":"André Kessler","doi":"10.1111/nph.70289","DOIUrl":"https://doi.org/10.1111/nph.70289","url":null,"abstract":"&lt;p&gt;Plants have evolved unique ways of processing environmental information to adjust their physiology, metabolism and growth to various environmental conditions. One such environmental condition is the consumption of their tissues by herbivores. Plants respond to herbivory with significant transcriptional and metabolic reconfigurations. Some of the metabolic changes, specifically those to secondary metabolism, can mediate increased resistance to the attacking herbivores, mostly through the increased production of toxic, antidigestive, antinutritive and repellant compounds or, simply, by altered compound composition or diversity (Kessler &amp; Baldwin, &lt;span&gt;2002&lt;/span&gt;). In all cases, plant responses can be strikingly specific to the attacking herbivore species or even the developmental stage of the attacker (Barrett &amp; Heil, &lt;span&gt;2012&lt;/span&gt;). The question of how these responses can be so specific and the role of induced response to herbivory in driving population-, community- and ecosystem-dynamics is a major driver of research in plant physiology and molecular biology as well as plant and chemical ecology (Kessler &amp; Kalske, &lt;span&gt;2018&lt;/span&gt;). In this Editorial, we introduce a Virtual Issue of &lt;i&gt;New Phytologist&lt;/i&gt; articles that highlight some of these recent developments in the study of herbivore-derived elicitors of plant responses.&lt;/p&gt;&lt;p&gt;Research into the mechanisms underlying induced responses to herbivory has long focused on the molecular response patterns associated with wounded plant tissue, known as damage-associated molecular patterns (DAMPs). This involves a complex wound signaling network that is driven by crosstalk between plant hormones, including ethylene, jasmonates and salicylates (Tanaka &amp; Heil, &lt;span&gt;2021&lt;/span&gt;). The extent to which each of the pathways is triggered relative to the others can explain the high specificity with which downstream metabolic responses are regulated. However, what are the primary triggers and how are alterations in responses regulated?&lt;/p&gt;&lt;p&gt;There is an increasing number of chemical elicitor compounds (compounds produced by organisms interacting with the plant) identified that either directly trigger or specifically alter standard wound responses. The most commonly studied elicitors are herbivore oral secretions and oviposition fluid-derived substances (Jones &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2022&lt;/span&gt;), and volatile organic compounds from neighboring plants (Kessler &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;). Both represent diverse groups of chemicals that provide specific information about organisms interacting with the plant and even allow the prediction of oncoming future herbivory or pathogen infection.&lt;/p&gt;&lt;p&gt;The study of elicitor-mediated herbivory-associated molecular patterns (HAMPs) (Mithoefer &amp; Boland, &lt;span&gt;2012&lt;/span&gt;) began with the identification of caterpillar saliva-derived β-glucosidase (Mattiacci &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;1995&lt;/span&gt;) and a caterpillar regurgitant-derived fatty acid-amino","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"247 2","pages":"431-435"},"PeriodicalIF":8.3,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.70289","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144315245","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}

{"title":"Automated extraction of leaf mass per area from digitized herbarium specimens.","authors":"Thais Vasconcelos,William N Weaver,Aly Baumgartner,Zoë Bugnaski,James Boyko","doi":"10.1111/nph.70292","DOIUrl":"https://doi.org/10.1111/nph.70292","url":null,"abstract":"The digitization of vast herbarium collections has made millions of plant specimen images freely available online, which can now be used to generate phenotypic datasets of unprecedented scope. Here, we assess the potential of computer vision tools to automate the extraction of predicted leaf mass per area (LMApred) from digitized herbarium specimens. We use an automated pipeline to extract leaf area and petiole width from 22 680 leaves, representing a phylogenetic informed sample of 1580 species of woody angiosperms. LMApred is estimated using a proxy equation that models the scaling relationship between petiole width and leaf mass. We assess potential sources of error in LMApred estimates and evaluate whether documented LMA-climate patterns are recovered using this dataset and phylogenetic comparative methods. Our LMApred dataset responds mainly to temperature and solar radiation and presents a positive correlation with latitude. The proxy equation, not the automated pipeline, is responsible for most of the error in LMApred estimates. Our pipeline underscores the power of combining herbarium digitization with new techniques for automated trait scoring. The increased size of datasets generated using this tool allows investigation of potential LMA-climate relationships with a geographically balanced sample while also utilizing comprehensive phylogenetic information.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"3 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144311591","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":"Degradation of AtSRC2 by SKP1/BTB/POZ domain effectors in Heterodera schachtii inhibits RBOHF via ROS and enhances infection","authors":"Ke Yao, Xin Zhang, Jinzhuo Jian, Yuese Ning, Chunhui Zhang, Jingwu Zheng, Duqing Wu, Lingan Kong, Wenkun Huang, Shiming Liu, Deliang Peng, Huan Peng","doi":"10.1111/nph.70281","DOIUrl":"https://doi.org/10.1111/nph.70281","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Upon pathogen infection, plants trigger a reactive oxygen species (ROS) burst to activate immunity. Although some effectors secreted by plant–parasitic nematodes are known to suppress ROS-mediated immunity, there are limited studies examining the regulation of respiratory burst oxidase homologs (RBOH)-dependent ROS pathways by these nematodes.</li>\u0000<li>Using developmental expression analysis, <i>in situ</i> hybridization, and immunohistochemical tests, we found that both <i>Hs28B03</i> and <i>Hs8H07</i> were expressed and secreted during the early parasitism by <i>Heterodera schachii</i>. Transgenic <i>Arabidopsis</i> plants were used to assess the role of Hs28B03 and Hs8H07 in <i>H. schachii</i> parasitism. Yeast two-hybrid was used to identify host targets in <i>Arabidopsis</i>.</li>\u0000<li>We identified Hs28B03 and Hs8H07 from <i>H. schachtii</i>, which play a crucial role in promoting nematode infection and parasitism, as well as inhibiting host immune responses. Hs28B03 and Hs8H07 harbor the SKP1/BTB/POZ domain and exhibit the capacity to mimic the host's SKP1 proteins, allowing them to regulate the ubiquitin pathway within the plant. Hs28B03 and Hs8H07 specifically target and degrade the host's AtSRC2 protein, inhibiting the Ca²⁺-dependent production of ROS mediated by RBOHF, enhancing <i>Arabidopsis</i> susceptibility to <i>H. schachtii</i>.</li>\u0000<li>In conclusion, nematodes can secrete effectors that mimic plant ubiquitination pathway components, suppressing ROS bursts via the RBOHF pathway, thereby facilitating parasitism.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"14 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144305483","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 innovations in plant immunity","authors":"Zhongshou Wu","doi":"10.1111/nph.70314","DOIUrl":"https://doi.org/10.1111/nph.70314","url":null,"abstract":"Toll/interleukin-1 receptor (TIR) domain-containing immune receptors are crucial for plant immunity, with recent advancements highlighting the enzymatic functions of TIR domains and their production of signaling molecules. TIR-catalyzed compounds interact with receptors to form functional modules that trigger the oligomerization of helper proteins, regulating Ca²⁺ influx and downstream signaling. Moreover, TIR proteins have been recognized not only as intracellular receptors for pathogenic effectors but also for their broader immune signaling capabilities. Although typical TIR-containing proteins are missing in monocots, both monocots and dicots exhibit conserved mechanisms in utilizing TIR proteins for immune signaling, underscoring their significance across diverse plant lineages. This review consolidates recent findings on TIR-initiated signaling, its intricate roles, and the fine-tuned regulatory mechanisms governing plant defense.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"14 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144305467","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}