Plant Direct最新文献

{"title":"Nature's Shield: Exploring Nonglandular Trichomes (NGT) as Key Players in Plant Defense Mechanisms.","authors":"Muhammad Ahmad, Sen Li, Yuming Dong, Songlin Yang, Yaru Wang, Lin Yang, Shanshan Fan, Kexin Shi, Mingshan Qu, Xingwang Liu, Huazhong Ren","doi":"10.1002/pld3.70118","DOIUrl":"10.1002/pld3.70118","url":null,"abstract":"<p><p>Trichomes are found on almost all terrestrial plants and are derived from epidermal cells. Nonglandular trichomes (NGTs) protect plants from environmental stress, such as pest and pathogen invasion, reduce water loss, and increase resistance to abiotic stressors, including UV radiation, cold, and extreme temperatures. Trichomes provide an excellent model system for studying the growth and differentiation of plant cells. Although several such genes that govern the specification and patterning of trichomes have been molecularly characterized in a few model plants, including <i>Arabidopsis thaliana</i>, most aspects of trichome initiation remain unclear. In this review, we summarize the structural and morphological characteristics of NGTs in diverse crops as well as report recent investigations providing insights into the regulation of NGT formation in plants. We also discuss how NGTs help plants resist various abiotic factors that impose multiple stresses on plant life. This review provides a foundation for understanding the valuable role of NGTs in protecting plants from multiple stresses.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 11","pages":"e70118"},"PeriodicalIF":2.8,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12647923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145637880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling Plant Recombination Patterns: Insights From Genome k-mers.","authors":"Mauricio Peñuela, Camila Riccio-Rengifo, Jorge Finke, Camilo Rocha","doi":"10.1002/pld3.70113","DOIUrl":"10.1002/pld3.70113","url":null,"abstract":"<p><p>Crossover recombination is a pivotal event that takes place during meiosis of germinal cells, leading to the rearrangement of parental chromosomes and generating novel allele combinations, thereby enhancing genetic diversity. This process holds significant importance for plant breeders as it enables the transfer of gene variants from one variety to another. Recent studies have explored diverse strategies to predict recombination events along chromosomes in key plant species, employing various types of genome features. In this study, the relationship between genome structure, quantified using k-mers, and crossover recombination is investigated. To facilitate this analysis, the Python package <i>kmerExtractor</i> is introduced; it uses frequency chaos game representation (FCGR) to count k-mers from genome fasta files and adds them as column features for subsequent analysis. This package is used to explore the genomes of one model and five crop plant species, namely, Arabidopsis, bean, maize, rice, sorghum, and tomato. The investigation reveals both positive and negative trends between 3-mers, 2-mers, and recombination rates. Furthermore, the information derived from k-mers was used to train regression-based machine learning models for predicting recombination rates along chromosomes. The results demonstrate the efficacy of using k-mer for predicting purposes, particularly for sorghum and tomato datasets, highlighting linear relationships between several k-mers and recombination events. We hope that this predictive strategy based on genomic sequence information can be useful for the development of new plant crosses.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 11","pages":"e70113"},"PeriodicalIF":2.8,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12646810/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145637917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leaf Anatomy, Volatile Metabolite Profile, and Cytotoxic Activity of the Endemic <i>Seseli tomentosum</i> Vis.: Insights Into Species-Specific Adaptations.","authors":"Elma Vuko, Sanja Radman, Juraj Kamenjarin, Ivana Bočina, Ema Topalović, Željana Fredotović","doi":"10.1002/pld3.70119","DOIUrl":"10.1002/pld3.70119","url":null,"abstract":"<p><p><i>Seseli tomentosum</i> Vis. is an endemic species distributed along the eastern coast of the Adriatic Sea. In this study, the leaf structure as observed by light and electron microscopy, the phytochemical composition of the volatile organic compounds, and the cytotoxic activity of <i>S. tomentosum</i> are presented. The secretory ducts located above and within the phloem and below the xylem part of the vascular bundle represent the first description of the leaf secretory structures of <i>S. tomentosum</i>. The essential oil and hydrosol were extracted from air-dried leaves by Clevenger distillation and analyzed by gas chromatography-mass spectrometry, combined with headspace solid-phase microextraction of volatiles from the hydrosol and fresh plant material. α-Amorphene, β-caryophyllene, germacrene D, β-cadinene, and α-copaene were the most abundant sesquiterpenes in the essential oil and fresh plant material. Among the monoterpenes, α-pinene was most abundant in the essential oil, limonene in fresh plant material, and α-terpineol in the hydrosol. Moderate cytotoxic activity of the methanolic extract of <i>S. tomentosum</i>, with higher inhibition of cell division observed in the human cervical cancer and osteosarcoma cell lines, and weaker activity in the healthy retinal pigmented epithelial and colon cancer cell lines, was detected using the MTS-based assay. With these results, we aim to highlight the potential of endemic plants, emphasizing the importance of studying species such as <i>S. tomentosum</i> and their contributions to biodiversity and human health as sources of bioactive compounds.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 11","pages":"e70119"},"PeriodicalIF":2.8,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12629911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145588531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative Transcriptomic and Phosphoproteomic Analysis Reveals Key Components of the SnRK1 Signaling Network in Rice.","authors":"Maria C Faria-Bates, Chandan Maurya, K Muhammed Jamsheer, Vibha Srivastava","doi":"10.1002/pld3.70120","DOIUrl":"10.1002/pld3.70120","url":null,"abstract":"<p><p>SnRK1 is an evolutionarily conserved protein kinase belonging to the SNF1/AMPK family of protein kinases that is central to adjusting growth in response to the energy status. Numerous studies have shown adaptive and developmental roles of SnRK1, but the understanding of the SnRK1 signaling network in monocots is limited. Using CRISPR/Cas9 mutagenesis to target the functional kinase subunits in rice, we carried out comprehensive phenotypic, transcriptomic, proteomic, and phosphoproteomic analyses of rice <i>snrk1</i> mutants displaying growth defects under normal and starvation conditions. These analyses revealed the role of SnRK1 signaling in controlling growth and stress-related processes in both energy-sufficient and energy-limited conditions and pointed to the subfunctionalization of SnRK1 kinase subunit genes. In addition to the classical protein targets of SnRK1, phosphoproteomics revealed novel targets including the key components of intracellular membrane trafficking, ethylene signaling, and ion transport. The upregulation of stress-related processes and suppression of growth-related processes in <i>snrk1</i> mutants correlated with their phenotypic defects. Overall, this study highlights a dual role of SnRK1 as a promoter of growth under favorable conditions and a critical regulator of adaptive response under stress conditions.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 11","pages":"e70120"},"PeriodicalIF":2.8,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12623061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145550609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Untargeted Proteomics Identifies Plant Substrates of the Bacterial-Derived ADP-Ribosyltransferase AvrRpm1.","authors":"Simranjit Kaur, Thomas Colby, Domenika Thieme, Carsten Proksch, Susanne Matschi, Ivan Matić, Lennart Wirthmueller","doi":"10.1002/pld3.70115","DOIUrl":"10.1002/pld3.70115","url":null,"abstract":"<p><p>One class of enzymes that plant pathogens employ to manipulate innate immunity and physiology of the infected cells is host-targeted ADP-ribosyltransferases. The bacterial pathogen <i>Pseudomonas syringae</i> uses its Type III secretion system to inject several effector proteins with ADP-ribosyltransferase activity into plant cells. One of them, AvrRpm1, ADP-ribosylates the plasma membrane-associated RPM1-INTERACTING PROTEIN 4 (RIN4) in <i>Glycine max</i> and <i>Arabidopsis thaliana</i> to attenuate targeted secretion of defense-promoting compounds. Substrate identification of host-targeted ADP-ribosyltransferases is complicated by the biochemical lability of the protein modification during plant protein extraction and in several cases requires prior knowledge of plant immune signaling pathways that are impaired by the ADP-ribosylating Type III effector. Using the AvrRpm1-RIN4 pair as a proof of concept, we present an untargeted proteomics workflow for enrichment and detection of ADP-ribosylated proteins and peptides from plant cell extracts that in several cases provides site resolution for the modification.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 11","pages":"e70115"},"PeriodicalIF":2.8,"publicationDate":"2025-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12620056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145541948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revealing the Application of Synchrotron-Based X-Ray Computed Tomography in Healthy Versus Unhealthy Interior Lodgepole Pine (<i>Pinus contorta</i> var. <i>latifolia</i>) Conelets.","authors":"Emelie Dykstra, Jarvis A Stobbs, Esteban Galeano, Barb R Thomas","doi":"10.1002/pld3.70117","DOIUrl":"10.1002/pld3.70117","url":null,"abstract":"<p><p>The reproductive cycle of interior lodgepole pine spans approximately 26 months, with seed cones initiating in late summer, followed by pollen conelets emerging the next spring when pollination occurs. Fertilization and cone maturation occur in the subsequent spring and fall. Successful pollination, critical for seed conelet retention, requires an ~80% success rate. In June 2020, 30 pine clones (genotypes), with contrasting conelet abortion rates, were selected from a production seed orchard in Alberta, Canada. Sixty conelets per clone (30 aborted and 30 healthy) were collected for synchrotron radiation-based microcomputed tomography (SR-μCT) analysis. A subset of two contrasting clones (1401 and 596) was selected for detailed study. Conelets were transported to the Canadian Light Source in Saskatoon, Saskatchewan, for SR-μCT Phase Contrast Imaging (PCI), where samples were mounted and scanned using a PCO Edge 5.5 sCMOS camera and analyzed using Avizo software to visualize internal structures. Results showed that healthy conelets in clones 1401 and 596 had greater tissue volume (248.8 and 251.9 mm³, respectively) and more organized cavity spaces than aborted conelets (64.7 and 102.1 mm³, respectively), with differential internal air space volume (clone 1401: 8.7 mm³ in aborted vs. 17.5 mm³ in healthy; clone 596: 6.9 mm³ in aborted vs. 11.5 mm³ in healthy). Overall, SR-μCT imaging demonstrated significant advantages over traditional methods of visualization by providing a nondestructive, high-resolution analysis of internal structures. In addition, this technology enhances our understanding of pine reproductive processes, improving management practices in seed orchards-the delivery system for tree improvement programs.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 11","pages":"e70117"},"PeriodicalIF":2.8,"publicationDate":"2025-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12620052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145541945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to \"Functional Relationships of Two NFU Proteins in Maintaining the Abundances of Mitochondrial Iron-Sulfur Proteins\".","authors":"","doi":"10.1002/pld3.70116","DOIUrl":"10.1002/pld3.70116","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1002/pld3.70081.].</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 10","pages":"e20007"},"PeriodicalIF":2.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12559806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145401593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Introduction to Network Analysis in Plant Biology.","authors":"Chamindika L Siriwardana, Ashleigh S Carlton, Thalia Lizeth Moncayo, Elizabeth A O'Bier, Laura E Bartley","doi":"10.1002/pld3.70114","DOIUrl":"10.1002/pld3.70114","url":null,"abstract":"<p><p>This beginner's guide is intended for plant biologists new to network analysis. Here, we introduce key concepts and resources for researchers interested in incorporating network analysis into research, either as a stand-alone component for generating hypotheses or as a framework for examining and visualizing experimental results. Network analysis provides a powerful tool to predict gene functions. Advances in and reduced costs for systems biology techniques, such as genomics, transcriptomics, and proteomics, have generated abundant omics data for plants; however, the functional annotation of plant genes lags. Therefore, predictions from network analysis can be a starting point to annotate genes and ultimately elucidate genotype-phenotype relationships. In this paper, we introduce networks and compare network-building resources available for plant biologists, including databases and software for network analysis. We then compare four databases available for plant biologists in more detail: AraNet, GeneMANIA, ATTED-II, and STRING. AraNet and GeneMANIA are functional association networks, ATTED-II is a gene coexpression database, and STRING is a protein-protein interaction database. AraNet and ATTED-II are plant-specific databases that can analyze multiple plant species, whereas GeneMANIA builds networks for <i>Arabidopsis thaliana</i> and nonplant species and STRING for multiple species. Finally, we compare the performance of the four databases in predicting known and probable gene functions of the <i>A. thaliana</i> Nuclear Factor-Y (NF-Y) genes. We conclude that plant biologists have an invaluable resource in these databases and discuss how users can decide which type of database to use depending on their research question.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 10","pages":"e70114"},"PeriodicalIF":2.8,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12560016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145401577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid and Cost-Effective Digital Quantification of RNA Editing and Maturation in Organelle Transcripts by Oxford Nanopore Target-Indexed-PCR (TIP) Sequencing.","authors":"Zhihua Hua","doi":"10.1002/pld3.70111","DOIUrl":"10.1002/pld3.70111","url":null,"abstract":"<p><p>RNA editing and maturation are critical regulatory mechanisms in plant organelles, yet their quantification remains technically challenging. Traditional Sanger sequencing lacks sensitivity and reproducibility, whereas advanced next-generation sequencing (NGS) approaches, such as rRNA-depleted long non-coding (lnc) RNA-seq or targeted amplicon-seq, involve high costs, complex workflows, and limited accessibility. To address these limitations, I developed a rapid and cost-effective long-read sequencing approach, termed Target-Indexed-PCR (TIP) sequencing, for digital quantification of RNA editing and intron retention events in targeted chloroplast transcripts. This method combines multiplexed high-fidelity PCR amplification with Oxford Nanopore sequencing and custom in-house Perl and Python scripts for streamlined data processing, including barcode-based demultiplexing, strand reorientation, alignment to a pseudo-genome, manual editing-site inspection, and splicing variant identification. As a proof of concept, TIP sequencing was applied to <i>ndhB</i> and <i>ndhD</i> transcripts, two chloroplast <i>NAD</i>(<i>P</i>)<i>H dehydrogenase</i> genes with the highest number of known editing sites in <i>Arabidopsis thaliana</i>. These transcripts were analyzed both in an inducible CRISPR interference (iCRISPRi) system targeting <i>MORF2</i>, a key RNA-editing factor, and in <i>MORF2-YFP</i> transgenic lines with either overexpression or co-suppression silencing. My findings revealed dose- and development-dependent impacts of <i>MORF2</i> on C-to-U editing efficiency. Moreover, I identified an accumulation of intron-retaining <i>ndhB</i> transcripts, specifically in Dex-treated iCRISPRi lines and in both <i>MORF2-YFP</i> overexpression and silencing rosette leaves, indicating impaired chloroplast splicing functions when <i>MORF2</i> expression is perturbed beyond an as-yet-undefined threshold. The platform achieves single-molecule resolution, robust reproducibility, and high read coverage across biological replicates at a fraction of the cost of lncRNA-seq. Collectively, this study establishes TIP sequencing as a versatile, scalable, and affordable tool for targeted post-transcriptional analysis in plant organelles and expands our understanding of <i>MORF2</i>'s role in chloroplast RNA maturation. By overcoming key limitations of existing approaches, TIP sequencing enables routine, site-specific quantification of post-transcriptional regulation in organelles, including RNA editing and splicing, making it broadly accessible to researchers studying plastid biology, stress responses, and organelle-nucleus communication.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 10","pages":"e70111"},"PeriodicalIF":2.3,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12537063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cm<i>SGT1</i>, Transcriptionally Regulated by CmWRKY21 and CmWRKY31, Improves Powdery Mildew Resistance in <i>Cucurbita moschata</i>.","authors":"Wei-Li Guo, Jin-Peng Zhao, Xue-Jin Chen, Bi-Hua Chen, Qing-Fei Li, Xin-Zheng Li","doi":"10.1002/pld3.70112","DOIUrl":"10.1002/pld3.70112","url":null,"abstract":"<p><p>Powdery mildew (PM), mainly caused by <i>Podosphaera xanthii</i>, is a severe destructive disease that threatens the production of cucurbit crops globally. Heterologous transformation has shown that the <i>CmSGT1</i> gene (suppressor of the G2 allele of skp1) improved PM resistance in tobacco. However, the function of the gene in pumpkins (<i>Cucurbita moschata</i>) is largely unknown. Herein, transient <i>CmSGT1</i> overexpression in pumpkin cotyledons inhibited the spore germination and mycelia growth of <i>P. xanthii</i> by inducing an increase in salicylic acid (SA) content, and exogenous SA intensified the inhibitory effect of the gene on the growth of <i>P. xanthii</i>. The β-glucuronidase activity of cotyledons transformed with the <i>CmSGT1</i> promoter was induced by PM and signaling molecules (gibberellic acid, ethephon, SA, abscisic acid, and methyl jasmonate). The yeast one-hybrid assay verified that transcription factor CmWRKY21, CmWRKY31, and CmWRKY75 proteins interact with the <i>CmSGT1</i> promoter. Transactivation analysis revealed that CmWRKY21 and CmWRKY31 significantly triggered the expression of <i>GUS</i> driven by the <i>CmSGT1</i> promoter under PM. Furthermore, transient co-overexpression of <i>CmWRKY21</i>/<i>CmWRKY31</i> and <i>CmSGT1</i> enhanced the inhibitory effect on the growth of <i>P. xanthii</i>. In conclusion, the <i>CmSGT1</i> gene is a PM resistance gene in pumpkin and is transcriptionally regulated by CmWRKY21 and CmWRKY31. Our study provides a reference for resistance breeding of pumpkins.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 10","pages":"e70112"},"PeriodicalIF":2.8,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12537062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}