New Phytologist最新文献

{"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}

{"title":"Solanoeclepin C, a root-secreted molecule converted by rhizosphere microbes to hatching factors for potato cyst nematodes.","authors":"Ryota Akiyama,Yui Kawano,Kosuke Shimizu,Soichiro Makino,Karen Akanuma,Haru Nagatomo,Masami Yokota Hirai,Yukihiro Sugimoto,Atsuhiko Kushida,Keiji Tanino,Masaharu Mizutani","doi":"10.1111/nph.70252","DOIUrl":"https://doi.org/10.1111/nph.70252","url":null,"abstract":"Eclepins are root-secreted compounds that induce the hatching of cyst nematodes. Solanoeclepin A (SEA) and B (SEB) have been isolated as potent hatching factors for potato cyst nematodes (PCNs). SEB is biosynthesized in roots, released into the rhizosphere, and converted into SEA by soil microorganisms. However, given that SEB and SEA exhibit comparable hatching-inducing activity toward PCNs, the ecological significance of microbial solanoeclepin metabolism in eclepin-mediated communication remains unclear. In this study, we identified solanoeclepin C (SEC), a previously unrecognized solanoeclepin secreted by tomato and potato roots. Structural analysis revealed that SEC is an acetylated derivative of SEB. Soil incubation experiments demonstrated that SEC is converted into SEB and subsequently into SEA. SEC exhibits  10 000-fold lower hatching-inducing activity than SEA. Gene expression analysis in hydroponically grown tomatoes showed that solanoeclepin biosynthesis is upregulated under nitrogen and phosphorus deficiencies, with nitrogen starvation having the strongest effect. Our results demonstrate that although SEC itself exhibits low hatching-inducing activity, it is converted by soil microorganisms into SEB and SEA, which are then exploited by PCNs to trigger their hatching. These findings reveal a previously unrecognized three-way interaction among plants, soil microbes, and nematodes mediated by solanoeclepins.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"34 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136789","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":"Comparative phylogenetic analyses of RNA editing in fern plastomes suggest possible adaptive innovations.","authors":"Blake D Fauskee,Li-Yaung Kuo,Tracy A Heath,Pei-Jun Xie,Kathleen M Pryer","doi":"10.1111/nph.70244","DOIUrl":"https://doi.org/10.1111/nph.70244","url":null,"abstract":"RNA editing in plant organelles is widely regarded as a neutral corrective mechanism, yet it persists as a complex, energetically costly process, requiring numerous nuclear-encoded pentatricopeptide repeat proteins. Ferns are the most diverse lineage of land plants that uniquely retain both cytidine-to-uridine (C-to-U) and uridine-to-cytidine (U-to-C) Berget RNA editing in their plastomes, offering a powerful system to investigate the evolutionary forces shaping both editing types. Two distantly related fern lineages - Hymenophyllaceae and Vittarioideae (Pteridaceae) - each containing sister sublineages with contrasting evolutionary rates, were selected for comparative analysis. Genomic and transcriptomic data were combined with bioinformatic and phylogenetic methods to identify RNA editing sites and investigate the evolutionary dynamics of both C-to-U and U-to-C editing in fern plastomes. Nonsynonymous edits were frequently lost, consistent with neutral evolution. By contrast, C-to-U edits at start codons and U-to-C edits at internal stop codons were evolutionarily conserved, displaying lower and more variable editing efficiencies that suggest these edits are regulated. C-to-U edits at start codons and U-to-C edits at internal stop codons are evolutionarily conserved and exhibit signatures of selective regulation, suggesting that they function as molecular checkpoints. These findings provide the strongest evidence to date that RNA editing in plants plays an adaptive role in modulating plastid gene expression.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"23 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136771","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":"At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways","authors":"Tino Köster, Peter Venhuizen, Martin Lewinski, Ezequiel Petrillo, Yamile Marquez, Armin Fuchs, Debashish Ray, Barbara A. Nimeth, Stefan Riegler, Sophie Franzmeier, Florencia S. Rodríguez, Federico E. Aballay, Rocío S. Tognacca, Hong Zheng, Timothy Hughes, Quaid Morris, Andrea Barta, Dorothee Staiger, Maria Kalyna","doi":"10.1111/nph.70221","DOIUrl":"https://doi.org/10.1111/nph.70221","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Gene expression in eukaryotes involves multiple regulatory layers. Following transcription, nascent RNAs undergo processing steps, including capping, splicing, polyadenylation, and chemical modification, to produce mature mRNAs (Yang <i>et al</i>., <span>2021</span>). Splicing removes introns from pre-mRNA and joins exons to generate the mature transcripts (Gilbert, <span>1978</span>). Although splicing is a highly regulated process ensuring specificity, it also shows remarkable plasticity. The spliceosome, the cellular machinery responsible for splicing, can recognize alternative splice sites, enabling a single gene to produce multiple transcript variants via alternative splicing.</p>\u0000<p>In plants, 40–70% of intron-containing genes undergo alternative splicing, underscoring its fundamental role in regulating gene expression during development and environmental responses (Filichkin <i>et al</i>., <span>2010</span>; Lu <i>et al</i>., <span>2010</span>; Marquez <i>et al</i>., <span>2012</span>; Chamala <i>et al</i>., <span>2015</span>). Alternative splicing not only produces diverse transcripts leading to different proteins but also generates noncoding isoforms, which may be rapidly degraded or remain stable, thus fine-tuning the total protein levels produced by a gene (Kalyna <i>et al</i>., <span>2012</span>; Petrillo, <span>2023</span>). Different types of alternative splicing events, such as exon skipping (ES), intron retention, and usage of alternative 5′ and 3′ splice sites, generate transcript diversity. While ES is common in animals, intron retention is most frequent in plants. Retained intron (RI) transcripts often remain in the nucleus, regulating protein levels during stress or developmental transitions (Kalyna <i>et al</i>., <span>2012</span>; Marquez <i>et al</i>., <span>2012</span>; Yap <i>et al</i>., <span>2012</span>; Boothby <i>et al</i>., <span>2013</span>; Leviatan <i>et al</i>., <span>2013</span>; Braunschweig <i>et al</i>., <span>2014</span>; Gohring <i>et al</i>., <span>2014</span>; Boutz <i>et al</i>., <span>2015</span>). Furthermore, exitrons (EIs), alternatively spliced internal regions within protein-coding exons, add another layer of complexity to the alternative splicing landscape (Marquez <i>et al</i>., <span>2015</span>; Staiger & Simpson, <span>2015</span>).</p>\u0000<p>The spliceosome ensures the accurate recognition of different pre-mRNA regions and intron removal, aided by numerous proteins. Among these proteins, two key groups stand out: serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs; Wachter <i>et al</i>., <span>2012</span>). Serine/arginine-rich proteins interact with the pre-mRNA and spliceosomal components, guiding spliceosome assembly at specific splice sites (Shepard & Hertel, <span>2009</span>). They contain one or two <i>N</i>-terminal RNA recognition motifs (RRMs), the most prevalent RNA-binding domain, and a C-terminal arginine/serine (","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"56 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144137125","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":"Single-cell transcriptomes reveal spatiotemporal heat stress response in pearl millet leaves.","authors":"Yarong Jin,Haidong Yan,Xin Zhu,Yuchen Yang,Jiyuan Jia,Min Sun,Atiqa Najeeb,Jinchan Luo,Xiaoshan Wang,Min He,Bin Xu,Xiang Li,Ziliang Luo,Chunli Mao,Dejun Huang,Gang Nie,Guangyan Feng,Zheni Xie,Xinquan Zhang,Lin Luo,Linkai Huang","doi":"10.1111/nph.70232","DOIUrl":"https://doi.org/10.1111/nph.70232","url":null,"abstract":"With the intensification of global warming, there is an urgent need to develop crops with enhanced heat tolerance. Pearl millet, as a typical C4 heat-tolerant crop, has mechanisms of heat tolerance at the cellular level which remain unclear. Constructed single-cell transcriptomic landscape of pearl millet leaves under heat stress and normal conditions, comprising 20 589 high-quality cells classified into five cell types. Vascular tissue cells were identified as the most critical cell type under heat stress, characterized by the highest number of differentially expressed genes and heat stress memory genes. Through single-cell WGCNA analysis combined with phenotypic and physiological analysis of heat stress memory gene UGT73C3 mutants and overexpression lines, we revealed the important role of heat stress memory genes in enhancing heat tolerance by promoting the clearance of reactive oxygen species accumulation. Our study provides a heat-tolerant crop leaf atlas revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"39 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136691","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":"Evolutionary-conserved RLF, a cytochrome b5-like heme-binding protein, regulates organ development in Marchantia polymorpha","authors":"Kentaro P. Iwata, Takayuki Shimizu, Yuuki Sakai, Tomoyuki Furuya, Hinatamaru Fukumura, Yuki Kondo, Tatsuru Masuda, Kimitsune Ishizaki, Hidehiro Fukaki","doi":"10.1111/nph.70181","DOIUrl":"https://doi.org/10.1111/nph.70181","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Heme is a porphyrin complex with a centrally coordinated iron atom. In plants, heme shares a metabolic pathway with Chl biosynthesis up to the production of protoporphyrin IX, after which ferrochelatase coordinates Fe<sup>2+</sup> to protoporphyrin IX (Roper & Smith, <span>1997</span>; Hederstedt, <span>2012</span>). In the Protein Data Bank (https://www.rcsb.org), which contains 222 415 proteins, 4272 protein chains have been identified as heme-binding proteins (HBPs) from entries containing heme types <i>b</i> and <i>c</i> (Li <i>et al</i>., <span>2011</span>). The binding of these HBPs to heme is maintained by the coordination of specific amino acids, such as histidine, within the apoprotein to the iron atoms of heme. In general, in various organisms, HBPs are essential for diverse biological processes such as steroid biosynthesis, aerobic respiration, and programmed cell death because of their role in electron transfer, substrate oxidation, and metal ion storage (Reedy & Gibney, <span>2004</span>; Layer <i>et al</i>., <span>2010</span>). In plants, HBPs, such as cytochrome <i>c</i>, which is involved in electron transfer during photosynthesis, and SOUL4, which is implicated in lipid metabolism within chloroplast fat droplets (plastoglobule), have demonstrated diverse physiological effects (Kerfeld & Krogmann, <span>1998</span>; Shanmugabalaji <i>et al</i>., <span>2020</span>). Recently, proteomic analyses in <i>Arabidopsis thaliana</i> have identified a variety of HBPs, such as basic/helix–loop–helix type nuclear transcription factors and intracellular signaling factors involved in GTPase activation (Shimizu <i>et al</i>., <span>2020</span>). These studies have revealed that HBPs function as intracellular signals regulating diverse physiological functions. However, it remains unclear how they are involved in plant organ development.</p>\u0000<p>One group of HBPs in plants is a family of proteins with a cytochrome <i>b</i><sub>5</sub>-like heme-binding domain (Cytb5-HBD). In plants, the metabolic pathways mediated by most Cytb5-HBD proteins are diverse, including fatty acid desaturation, lignin biosynthesis, and nitrate reduction (Nagano <i>et al</i>., <span>2012</span>; Gou <i>et al</i>., <span>2019</span>). The genome of <i>A. thaliana</i> has 15 proteins with a Cytb5-HBD, including five members of the cytochrome <i>b</i><sub>5</sub> family (At1g26340 (CB5A), At2g32720 (CB5B), At2g46650 (CB5C), At5g48810 (CB5D), and At5g53560 (CB5E)) (Maggio <i>et al</i>., <span>2007</span>), one cytochrome <i>b</i><sub>5</sub>-like protein (At1g60660 (CB5LP)), four membrane-associated progesterone binding proteins (At2g24940 (MAPR2), At3g48890 (MAPR3), At4g14965 (MAPR4), and At5g52240 (MAPR5)) (Yang <i>et al</i>., <span>2005</span>), two Δ-8 sphingolipid desaturases (At3g61580 (SLD1) and At2g46210 (SLD2)) (Sperling <i>et al</i>., <span>1998</span>), two nitrate reductases (At1g77760 (NR1) and At1g37130 (NR2)) (Cheng <i>et al","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"135 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144133621","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 baldcypress genome provides insights into the adaptive evolution of flooding stress tolerance.","authors":"Ying Yang,Chaoguang Yu,Jianfeng Hua,Ziyang Wang,Tingting Chen,Qinglin Zhu,Hui You,Lei Xuan,Chengyi Tang,Yunlong Yin","doi":"10.1111/nph.70230","DOIUrl":"https://doi.org/10.1111/nph.70230","url":null,"abstract":"The evolutionary history of gymnosperms suggests that most species struggle in wet environments. However, baldcypress (Taxodium distichum var. distichum) thrives in wetlands, making it a prime candidate for studying flood tolerance in gymnosperms. Our study aimed to explore the genetic basis of this flood tolerance. We accomplished the first chromosome-level genome assembly of baldcypress. Using Oryza sativa, Arabidopsis thaliana, baldcypress, and Taxus wallichiana, we compared gene expression, regulatory elements, and gene expansions between flood-tolerant and flood-intolerant plants. The baldcypress genome spans c. 7.82 Gb, containing 44 010 protein-coding genes. We identified 409 commonly upregulated and 668 commonly downregulated orthogroups, representing conserved flood-stress responses. Additionally, 352 orthogroups contained more upregulated genes in tolerant plants. Baldcypress appears to employ different evolutionary strategies than rice to withstand flooding. Both strategies involve the evolution of ERF-VII transcriptional activation and antioxidant pathways. However, each species expanded distinct nodes within these pathways. Additionally, the evolution of spliceosome genes in baldcypress and energy-producing genes in rice further reflects their differing evolutionary strategies. This study underscores the diversity and commonality of mechanisms underlying plant flood responses and tolerance, providing theoretical guidance for research on the genetic improvement of plant flooding tolerance.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"57 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122300","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":"Hygroscopic stem reshaping promotes long-distance plant dispersal.","authors":"Yuhong Luo,Zhenjie Guo,Jiquan Chen,Wenyuan Ruan,Xingliang Xu,Le Li,Yufan Bao,Nuo Xu,Xiaoping Xin,Keke Yi,David J Eldridge,Yuchun Yan","doi":"10.1111/nph.70225","DOIUrl":"https://doi.org/10.1111/nph.70225","url":null,"abstract":"Cleistogenes squarrosa is a pioneer tumble plant widely distributed across the Eurasian steppes. It achieves long-distance wind dispersal through stem reshaping. However, the underlying ecological adaptation mechanisms of this dispersal strategy remain unexplored. Combining with field and laboratory observations, we revealed that four coordinated processes - plant phenology, cell wall development, water supplies, and aerodynamic adaptations - interactively facilitate the anemochory of this endemic species in the Eurasian steppes. Specifically, the development of the cell wall with heterogeneous microfibril arrangement plays a critical role in hygroscopic stem reshaping, which occurs in synchrony with seed maturation. Remarkably, the subsequently dry and windy season perfectly follows these two synchronized processes, providing ideal dehydration conditions for stem reshaping and enhancing aerodynamic efficiency for long-distance dispersal. This model for long-distance dispersal innovatively showcases how microscopic cell wall structure propels macroscopic dispersal capabilities and environmental adaptation, ultimately enhancing ecosystem resilience to environmental changes. Collectively, these results indicate the potential for promoting the introduction and cultivation of C. squarrosa to support the restoration of degraded and arid ecosystems. Moreover, this newly identified mechanism provides a valuable direction for future research aimed at developing herbaceous plant varieties with improved dispersal capabilities through molecular breeding techniques.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"137 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122307","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 novel approach for detecting molecular O2 at the subcellular level in plants.","authors":"Ole Pedersen","doi":"10.1111/nph.70248","DOIUrl":"https://doi.org/10.1111/nph.70248","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"137 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122308","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}