Plant Direct最新文献

{"title":"Genomic and Functional Characterization of Sunflower Endophytes Reveals Mechanisms of Drought Tolerance and Growth Promotion.","authors":"Muritala Muhammed, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola","doi":"10.1002/pld3.70184","DOIUrl":"10.1002/pld3.70184","url":null,"abstract":"<p><p>Drought severely limits sunflower (<i>Helianthus annuus</i> L.) productivity, necessitating sustainable microbial strategies to enhance plant resilience. Endophytic bacteria modulate plant stress responses through diverse plant growth-promoting (PGP) traits. This study characterized <i>Pseudomonas protegens</i> M4 and <i>Citrobacter braakii</i> M34 and evaluated their individual and combined effects on sunflower drought tolerance. Greenhouse experiments assessed inoculation with M4, M34, and their consortium (M4 + M34) under optimal (100% field capacity, FC) and drought conditions (75%-25% FC). Initial taxonomic identification based on 16S rRNA gene sequencing was further refined using whole-genome sequencing (WGS) for high-resolution classification and functional analysis. Genomic annotation and antiSMASH analysis revealed key PGP pathways in both strains, including enzymes involved in ethylene regulation, phosphate solubilization, biosynthesis of auxin-like compounds, osmoprotectant production, and reactive oxygen species detoxification, alongside shared and strain-specific secondary metabolite gene clusters. Under drought conditions, M4 primarily enhanced growth-related traits such as shoot development and leaf area, whereas M34 was associated with physiological stress tolerance indicators. The consortium M4 + M34 exhibited synergistic effects, significantly increasing the chlorophyll content, relative water content, and proline accumulation while reducing electrolyte leakage. Principal component analysis further confirmed the consortium's superior performance. These findings highlight the potential of genomically and functionally characterized endophytic bacterial consortia as effective bioinoculant strategies for improving sunflower productivity under water-limited conditions.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 7","pages":"e70184"},"PeriodicalIF":2.8,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13372015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456475","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":"The Metabolic Awakening of Barley Seedlings: A Time-Resolved View of How Germination and Light Shape Tissue-Specific Metabolic Networks.","authors":"Claude Y Hamany Djande, Paul A Steenkamp, Ian A Dubery","doi":"10.1002/pld3.70185","DOIUrl":"10.1002/pld3.70185","url":null,"abstract":"<p><p>Integration of internal metabolism with environmental cues is essential for successful establishment and survival of seedlings, with light an important mediator of the transition from skotomorphogenesis to photomorphogenesis. However, detailed knowledge of the metabolic events associated with this critical transition in developing tissues of barley germlings/seedlings is currently lacking. We systematically mapped the temporal and tissue-resolved metabolic reprogramming in seedlings grown under light/dark photoperiod and complete darkness, using nontargeted high-resolution LC-MS metabolomics to characterize seeds, shoots, and roots at 3-9 days postimbibition. Dark-grown seedlings displayed allocation of resources to length rather than density. Multivariate analyses revealed distinct, light-induced metabolic reprogramming in each tissue type. Among 192 annotated metabolites, seed metabolism was dominated by mobilization and pre-emptive defense priming, with roots developing energy-centered networks. In darkness, shoots directed metabolism toward rapid elongation and synthesis of defensive hordatine isoforms A and B, alongside linolenic acid and tryptophan derivatives. Light triggered metabolic switches where shoots allocated resources toward photoprotective flavonoids and antifungal hordatine C. This work provides the first spatiotemporal metabolic atlas of metabolic awakening in germinating barley seeds and seedling establishment based on data-driven insights into metabolic pathways. It redefines skotomorphogenesis as an active escape-and-defense strategy and offers insight into photomorphogenesis in support of tissue-specific metabolomic differentiation.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 7","pages":"e70185"},"PeriodicalIF":2.8,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13357377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437720","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":"Evidence That Sri Lanka Is the Origin of a Rare Nematode Resistance Gene in Rice.","authors":"S Yashodha S D De Silva, Ceilan Handy, Eduard Roumen, M L A M S Munasinghe, Adam H Price","doi":"10.1002/pld3.70182","DOIUrl":"10.1002/pld3.70182","url":null,"abstract":"<p><p><i>Meloidogyne graminicola</i> is a destructive and widespread pest in tropical rice-growing systems, whereas resistance in <i>Oryza sativa</i> remains exceptionally rare. A major quantitative trait locus (QTL) associated with resistance has previously been identified at the distal end of chromosome 11 in the resistant varieties, LD 24 (Sri Lanka) and KPM (Thailand). In this study, we combined bioinformatic and molecular approaches to characterize this locus and phenotypically screened a collection of Sri Lankan landraces to investigate the distribution and potential origin of resistance. We identified a rare 7-bp deletion in LOC_Os11g44580 completely associated with the resistance phenotype, along with a notable occurrence of heterozygosity at this locus in some accessions. The deletion is located within a genomic region recently reported to harbor the resistance gene <i>MG1</i> in the Chinese cultivar Zhonghua 11. Among 121 Sri Lankan landraces screened using the 7-bp deletion marker, eight accessions carried the deletion, whereas 12 were heterozygous; all exhibited resistance to Mg. Notably, the majority of resistant landraces belonged to the distinct Sri Lankan subgroup <i>indica 2</i> and were predominantly collected from the Northern Province of Sri Lanka, suggesting a potential geographic origin of this resistance-associated allele. This study identifies 20 novel resistant varieties and highlights a regional concentration of resistance, providing valuable resources for breeding and insights into the evolutionary basis of nematode resistance in rice.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 7","pages":"e70182"},"PeriodicalIF":2.8,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13357382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437759","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":"Insights Into the Regulation of Salt Tolerance by Flavonoid and Cyanoamino Acid Metabolism in Sorghum-Sudangrass Hybrids.","authors":"Yue Shi, Zili Liu, Shuancheng Liu, Wenjuan Chai, Junxiang Mu","doi":"10.1002/pld3.70186","DOIUrl":"10.1002/pld3.70186","url":null,"abstract":"<p><p>Clarifying the molecular mechanisms underlying salt tolerance in high-performing sorghum-sudangrass hybrids can aid the identification of salt tolerance genes. Here, the previously screened salt-tolerant sorghum-sudangrass hybrid variety MN9 and the salt-sensitive variety MN4 were grown in sand-filled pots. At the five-leaf stage (21 days after sowing), seedlings were subjected to NaCl solutions at six concentrations (0, 70, 140, 210, 280, and 350 mM). After 72 h of treatment, mature leaves were collected to determine physiological indices across all concentrations. We then conducted transcriptome sequencing of leaf samples from the 0 mM (control) and 280 mM (high salt stress) treatments, and the sequencing results were validated by qRT-PCR. Under salt stress, MN9 maintained a high relative chlorophyll content (SPAD value), accumulated significantly more proline than MN4, and showed high peroxidase (POD) activity throughout the treatment period. Transcriptome profiling revealed 4340 differentially expressed genes (DEGs) between the salt-tolerant and salt-sensitive varieties under salt stress, including 2624 upregulated and 1716 downregulated genes. KEGG enrichment analysis showed that, under control conditions, genes in both varieties were enriched in the photosynthesis pathway; SORBI_3001G147400 (<i>petF</i>) supported normal photosynthetic function. Following salt stress, DEGs were predominantly enriched in biosynthesis of secondary metabolites, cyanoamino acid metabolism, and flavonoid biosynthesis. Key flavonoid biosynthesis genes (e.g., <i>CHS</i>, <i>CYP98A</i>, and <i>CYP75B1</i>) were specifically induced. In the cyanoamino acid metabolism pathway, SORBI_3004G335500 (<i>HNL</i>) and SORBI_3001G012400 (<i>UGT85B1</i>) were strongly expressed in MN9. The hydroxynitrile lyase gene <i>HNL</i> (SORBI_3004G335500) was experimentally verified as a key regulator of salt tolerance in sorghum-sudangrass hybrid.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 7","pages":"e70186"},"PeriodicalIF":2.8,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13346354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148423448","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":"Functional Genomics of Sulfur Metabolism in Rice: Insights From Transgenic and MicroRNA-Based Strategies.","authors":"Fawad Rauf, Hakim Zamir, Hussam Ahmad, Daud Ali Shah, Shahrukh Khan, Zameer Hussain Jamali, Sada Tanzil, Mohammed S Alotaibi, Usman Zulfiqar, Dilnoza Sotiboldiyeva, Dilshod Rakhmanov, Mayank Anand Gururani, Shakal Khan Korai","doi":"10.1002/pld3.70181","DOIUrl":"10.1002/pld3.70181","url":null,"abstract":"<p><p>Sulfur (S) is an essential macronutrient that plays critical roles in plant growth, redox homeostasis, stress adaptation, and immunity. In rice (<i>Oryza sativa</i>), sulfur deficiency is becoming increasingly common due to modern agricultural practices, yet the molecular regulation of sulfur metabolism remains incompletely understood. Recent advances in functional genomics have provided new insights into the mechanisms governing sulfur uptake, transport, assimilation, and downstream metabolic regulation. This review synthesizes current knowledge of sulfur metabolism in rice, with particular emphasis on transgenic and microRNA-based approaches. We discuss the functions of sulfate transporters, sulfur assimilation enzymes, and sulfur-containing metabolites such as glutathione in regulating sulfur homeostasis, redox balance, and stress responses. Particular attention is given to the conserved miR395 regulatory module, which coordinates sulfur assimilation and allocation through posttranscriptional regulation of ATP sulfurylase genes. Evidence from functional genomics studies demonstrates that sulfur metabolism is closely integrated with redox signaling, stress tolerance, and plant immunity. Collectively, these findings support a view of sulfur metabolism as a dynamic regulatory network rather than a linear nutrient-assimilation pathway. We further highlight key knowledge gaps, emerging research opportunities, and future directions for applying functional genomics to improve sulfur use efficiency and resilience in rice. This review provides a framework for advancing both the fundamental understanding and translational application of sulfur metabolism in sustainable rice production.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 7","pages":"e70181"},"PeriodicalIF":2.8,"publicationDate":"2026-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13333657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437797","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":"<i>FLOWERING LOCUS T</i> Genes <i>MtFTb1 and MtFTb2</i> Act Redundantly to Promote Flowering Under Long Days in <i>Medicago truncatula</i>.","authors":"Soledad Perez Santangelo, Richard C Macknight","doi":"10.1002/pld3.70178","DOIUrl":"10.1002/pld3.70178","url":null,"abstract":"<p><p>Flowering time is a crucial agronomic trait affecting yield and plant performance in different climates and photoperiods. While the molecular pathways regulating photoperiodic flowering are well-characterized in <i>Arabidopsis</i> and cereals, they remain poorly understood in many other groups of plants. <i>FLOWERING LOCUS T (FT)</i> genes are key components regulating the transition from vegetative to reproductive stages. In the legume <i>Medicago truncatula</i>, a forage crop, six FT orthologs are present. To date, only the role of <i>MtFTa1</i> has been described, promoting flowering after prolonged exposure to cold (vernalization), while the other five remain unclear. Here we show that <i>MtFTb1</i> and <i>MtFTb2</i> together are essential for flowering under long-day (LD) photoperiods. Using CRISPR/Cas9, we generated <i>Mtftb1</i> single mutants and <i>Mtftb1/2</i> double mutants. <i>MtFTb1</i> and <i>MtFTb2</i> genes act redundantly and are required to up-regulate <i>MtFTa1</i> under vernalized LD conditions. While <i>Mtftb1</i> mutants flower normally under short-day (SD) and LD conditions, <i>Mtftb1/2</i> mutants are delayed specifically under LD but retain a vernalization response. Transcriptomic analysis of wild-type and <i>Mtftb1/2</i> mutants shows <i>MtFTb1/2</i> are essential for MADS-box gene upregulation and modulate known and candidate flowering regulators under LD. These findings advance our understanding of flowering time control in legumes and may inform strategies to improve forage crop productivity.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 6","pages":"e70178"},"PeriodicalIF":2.8,"publicationDate":"2026-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13276279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148295948","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":"CISP, an Intrinsically Disordered Cold-Inducible Barley Protein, Functions as a Small RNA Chaperone.","authors":"Yutaro Okumura, Md Maksudul Haque, Shin-Ichiro Kidou","doi":"10.1002/pld3.70179","DOIUrl":"10.1002/pld3.70179","url":null,"abstract":"<p><p>Low temperatures are a major environmental stress that limits plant growth and development. Understanding the molecular mechanism of cold tolerance is therefore essential for improving crop performance through molecular breeding. In this study, we focused on CISP, a small, previously uncharacterized protein, specifically induced in barley roots under low temperature conditions, and investigated its potential role in cold tolerance. Heterologous expression of CISP in <i>Escherichia coli</i> enhanced late-phase bacterial growth at low temperatures compared with the wild-type strain. Similarly, overexpression of CISP in <i>Arabidopsis thaliana</i>, which lacks an apparent ortholog, improved seedling growth under low temperature conditions. These results suggest that CISP can promote growth of heterologous organisms used in this study at low temperature environments. To investigate its molecular function, we performed RNA chaperone assays using RNA beacons that tend to form stable secondary structures. CISP reduced the formation of RNA secondary structures and facilitated their destabilization, indicating RNA chaperone-like activity. CISP is a basic, low-molecular-weight protein containing an intrinsically disordered region (IDR) at its N-terminus but lacking canonical RNA-binding domains such as the cold shock domain (CSD) or RNA recognition motif (RRM). Our findings therefore suggest that CISP may represent a previously uncharacterized type of RNA chaperone. This study provides new insights into the structure and function of CISP and its potential contribution to cold tolerance in barley.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 6","pages":"e70179"},"PeriodicalIF":2.8,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13261088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148252623","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":"Under the Cover of Darkness: A Transcriptomic Exploration of Clubroot During the Night.","authors":"Andrea Garvetto, Susann Auer, Freia Benade, Michaela Hittorf, Jutta Ludwig-Müller, Sigrid Neuhauser","doi":"10.1002/pld3.70176","DOIUrl":"10.1002/pld3.70176","url":null,"abstract":"<p><p><i>Plasmodiophora brassicae</i> (Phytomyxea, Rhizaria) is the etiological agent of clubroot disease, one of the most important diseases of Brassicaceae crops. Alteration of metabolism and hormone homeostasis leads to the formation of tumor-like galls in the roots of affected plants. Host plant energy metabolism, defense, and developmental processes are under strong temporal control and the very same processes are affected by clubroot. For the first time, this study uses time-resolved transcriptome analyses to explore how <i>P. brassicae</i> affects <i>Arabidopsis thaliana</i> in the night during intermediate (14 days after inoculation; DAI) and late (21 DAI) infection. Day-night differences in gene expression were more pronounced in younger rather than older plants in our differential gene expression (DGE) analysis. Consequently, intermediate phases of infection showed more day-night differences than later ones. Clustering of differentially expressed genes (DEGs) in functional categories highlighted how some of the typical processes known to be disrupted by clubroot infection are more significantly affected in the night and also uncovered some disrupted exclusively in the night. RNA modification stood out as the most unambiguously upregulated process in infected <i>Arabidopsis</i> roots in the night. Analysis of the interaction between clubroot infection and diel oscillations in gene expression detected modifications in the rhythmicity of central circadian clock components during the infection. We discuss our findings in the context of manipulation of plant defense and metabolism, identifying targets for experimental validation and highlighting potential new lines of investigation of our time-resolved datasets to better understand the interaction between <i>P. brassicae</i> and its host.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 6","pages":"e70176"},"PeriodicalIF":2.8,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13247141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148219373","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":"Small Signaling Peptides in <i>Sorghum bicolor</i>: Integrating Phylogeny and Gene Expression to Characterize Roles in Stem Development.","authors":"Evan Kurtz, Brian McKinley, John Mullet","doi":"10.1002/pld3.70177","DOIUrl":"10.1002/pld3.70177","url":null,"abstract":"<p><p>Small signaling peptides (SSPs) are important regulators of plant growth, development, and responses to biotic and abiotic stress, yet their role in the C4 grass <i>Sorghum bicolor</i> is largely uncharacterized. To help fill this knowledge gap, 219 sorghum genes that encode SSPs were identified based on SSP sequences previously identified in <i>Arabidopsis thaliana</i>, <i>Zea mays</i>, <i>Oryza sativa</i>, <i>Triticum aestivum</i>, and <i>Brachypodium distachyon</i>. The 219 sorghum SSP-encoding genes were assigned to 19 gene families, analyzed for the presence of motifs, and aligned with genes that encode SSPs in other plants using phylogenetic analysis. Sorghum genes in 12 of the 19 SSP gene families had not been previously characterized. Expression of the 219 SSP-encoding genes in sorghum organs, during stem development, and in stem tissues and cell types revealed distinct spatial, temporal, and developmental patterns of expression. Genes associated with the <i>SbCEP</i> and <i>SbRGF</i> families were preferentially expressed in roots, whereas <i>SbEPF</i> genes were expressed in stem epidermal and pith parenchyma cells and panicles. The expression of genes during bioenergy sorghum stem growth and development was investigated because stems account for ~80% of harvested biomass and serve as conduits for water and nutrient transport between leaves and roots. During stem development, 28 SSP genes in several families (<i>CLE</i>, <i>EPF</i>, <i>CEP</i>, <i>GASS</i>, <i>PSY</i>, <i>ES</i>, <i>PSK</i>, <i>CAPE</i>, <i>POE</i>) were expressed at higher levels in zones of cell proliferation. For example, the TDIF homologs S<i>bCLE41</i> and <i>SbCLE42</i> were expressed at high levels in nascent stem nodes where they may regulate vascular bundle cambial activity and cell differentiation. A different set of 15 genes in the <i>CIF</i>, <i>POE</i>, <i>CAPE</i>, <i>PSY</i>, <i>CEP</i>, <i>RALF</i>, and <i>CLE</i> families were expressed at higher levels in zones of stem tissue differentiation highlighted by elevated expression of five <i>SbRALFR</i>s in the stem nodal plexus. Cell type-specific expression of many sorghum genes that encode SSPs was observed in fully elongated internodes indicating gene expression is regulated with high spatial resolution. Overall, the results provide a foundation of information for analysis of SSP function in sorghum that can be integrated with knowledge of sorghum gene regulatory networks to modulate traits important for production of sorghum crops.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 6","pages":"e70177"},"PeriodicalIF":2.8,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13247307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148219411","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":"Stage-Specific RNA Turnover Drives Small RNA Dynamics in <i>Arabidopsis</i>-<i>Colletotrichum</i> Interactions.","authors":"Carolina E Armijos, Thi-Thu-Huyen Chu, Richard J O' Connell, Blake C Meyers, Patricia Baldrich","doi":"10.1002/pld3.70172","DOIUrl":"10.1002/pld3.70172","url":null,"abstract":"<p><p>Small RNAs (sRNAs) are key regulators of plant defense and have been implicated in cross-kingdom interactions with pathogens. The hemibiotrophic fungus <i>Colletotrichum higginsianum</i> infects <i>Arabidopsis thaliana</i> through three stages: appressorial penetration, biotrophy, and necrotrophy. However, the dynamics of fungal and plant sRNA populations across these three stages have not been elucidated. Using high-throughput sequencing, we profiled sRNAs from <i>A. thaliana</i> and <i>C. higginsianum</i> during in planta appressorium (PA), biotrophic (BP), and necrotrophic (NP) phases, and compared them to fungal mycelia (MY) and in vitro appressoria (VA). Our analyses revealed stage-specific patterns in sRNA accumulation in both the plant and the pathogen. In <i>C. higginsianum</i>, sRNAs were dominated by 29 nt species in PA, BP, MY, and VA, but shifted to 18 nt in NP, consistent with RNA degradation during host cell death. In <i>A. thaliana</i>, sRNAs transitioned from 30-33 nt in PA/BP to a 21 nt dominant peak in NP. Also, TE-derived siRNAs and other regulatory sRNAs (miRNAs, ncRNA, snoRNAs, and snRNAs) declined during NP. A total of 62 host miRNAs showed differential accumulation, including core plant developmental regulators active across infection stages, and stage-specific miRNAs such as miR396, miR170/171, miR472, and miR858b. tRFs displayed opposite trends in host and pathogen: fungal tRFs declined in NP, while host tRFs increased. These tRFs' contrasting trends may reflect differences in RNA processing or degradation between host and pathogen. Our results provide new insights into RNA-mediated plant-fungal interactions.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 ","pages":"e70172"},"PeriodicalIF":2.8,"publicationDate":"2026-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13175767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964720","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}