Plant Direct最新文献

{"title":"Gene Expression Patterns Regulating Peanut Reproductive Phenology.","authors":"Carlos Henrique Cardon, Adnan Kivanc Corut, Ye Chu, Jason Wallace, Ran Hovav, Peggy Ozias-Akins","doi":"10.1002/pld3.70170","DOIUrl":"https://doi.org/10.1002/pld3.70170","url":null,"abstract":"<p><p>Peanut reproduction is foundational for crop yield, breeding, and evolution. However, gene regulation underlying peanut flowering pattern and timing has received limited attention. Cultivated peanut (<i>Arachis hypogaea</i> L.) shows two distinct flowering patterns between two subspecies, with ssp. <i>hypogaea</i> lacking flowers on the main stem and ssp. <i>fastigiata</i> having them. Understanding the gene regulatory networks that control peanut flowering will inform the genetic pathways impacting peanut reproduction, phenology, and yield. To this end, we measured whole-transcriptome gene expression of leaves and shoot tips (meristem) at six plant growth stages from Tifrunner, a peanut cultivar belonging to ssp. <i>hypogaea</i>, and GT-C20, a peanut germplasm belonging to ssp. <i>fastigiata</i>. Overall gene expression was distinct between the two genotypes in both tissue types. Flowering regulators including <i>AhFT</i>, <i>AhSOC1</i>, <i>AhAGL42</i>, and <i>AhSPL3</i> were differentially expressed in both the main and lateral stem at the time of flowering initiation (T3-first bloom). This indicates that positive regulation of these flowering regulators drives the distinct pattern of flowering on the main stem in GT-C20. Meanwhile, the differential expression of two <i>RING-finger E3 ubiquitin ligases</i> was identified between the two genotypes, indicating that the PAF1-complex (PAF1C) may contribute to the lack of flowering on the main stem of Tifrunner. Gene co-expression network analysis indicates that gibberellic acid (GA) and jasmonic acid (JA) pathways are involved in reproductive regulation. These results provide insight into how flowering physiology is differentially controlled between the two peanut subspecies and provide a launching point for additional research in peanut floral development.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 ","pages":"e70170"},"PeriodicalIF":2.3,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147841945","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 Structure of the Chemotype Determining Locus in <i>Cannabis sativa</i>.","authors":"Keith Allen, Anthony Torres, Reginald Gaudino","doi":"10.1002/pld3.70166","DOIUrl":"https://doi.org/10.1002/pld3.70166","url":null,"abstract":"<p><p>The chemical phenotype (chemotype) of <i>Cannabis sativa</i> is defined by the ratio of cannabidiolic acid (CBDA) to Δ9-tetrahydrocannabinolic acid (THCA). Although the Mendelian segregation of these traits suggests a single-locus biallelic system, recent sequencing and phylogenetic evidence indicate they are encoded by two distinct, tightly linked genes. The precise genomic architecture of this region, known as the <i>B</i> locus, has remained poorly defined. In this study, we analyzed recently released high-quality <i>Cannabis</i> reference genomes to resolve the structure of the <i>B</i> locus. Our results demonstrate that this region functions as a supergene, characterized by suppressed recombination that facilitates Mendelian-like switching between phenotypic states. Comparative genomic analysis reveals substantial structural polymorphism within the locus, including significant variations in gene copy number and large-scale insertions/deletions (indels). Furthermore, we functionally characterized three previously unstudied members of the cannabinoid oxidocyclase family. We find that these enzymes primarily catalyze the production of cannabichromenic acid (CBCA), reinforcing the model that cannabinoid profile is dictated specifically by the presence and expression of THCAS or CBDAS. Finally, we mapped the expression profile of the entire berberine bridge enzyme (BBE) family, identifying widespread expression across plant tissues, including in glandular trichomes. Collectively, these findings resolve the genomic architecture of the <i>B</i> locus, clarify the enzymatic basis of cannabinoid profile determination, and establish a framework for understanding the evolutionary maintenance of chemotype diversity in <i>C. sativa</i>.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 5","pages":"e70166"},"PeriodicalIF":2.3,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13128303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147819749","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":"Subgenomic Distribution and Herbicide Cross-Resistance of <i>ALS</i> Gene Mutations in Allohexaploid <i>Echinochloa crus-galli</i>.","authors":"Luan Cutti, Guilherme Menegol Turra, Filipi Mesquita Machado, Estéfani Sulzbach, Paula Sinigaglia Angonese, Catarine Markus, Todd A Gaines, Aldo Merotto","doi":"10.1002/pld3.70168","DOIUrl":"https://doi.org/10.1002/pld3.70168","url":null,"abstract":"<p><p>Herbicide target site resistance in polyploid species is more complex than in diploids due to potential subgenome interactions. This study characterized mutations in the <i>ALS</i> gene across distinct subgenomes of hexaploid <i>Echinochloa crus-galli</i> and evaluated the cross-resistance patterns conferred by each mutation to various ALS-inhibiting herbicides. <i>E. crus-galli</i> populations were screened, and dose-response curves were performed with ALS inhibitors from different chemical groups. The <i>ALS</i> gene copies of each subgenome (A, B, and C) were sequenced. Copy number variation, global relative expression, and the specific relative expression of <i>ALS</i> gene from each subgenome were performed. The mutations Ala122Thr, Ala205Asn, and Ser653Asn conferred resistance only to imazethapyr, whereas Trp574Leu to imazethapyr, penoxsulam, bispyribac-sodium, and nicosulfuron, when considered the label rate. <i>ALS</i> mutations were more frequent in subgenome A, but <i>ALS</i> from subgenome C had the highest expression. Biotypes with the same mutation showed different resistance level to herbicides. The biotype SAOJER-01 had Trp574Leu mutation in subgenome C and was 22 times more resistant to imazethapyr and penoxsulam than CAMAQ-01, which had the same Trp574Leu mutation in subgenome A. Both SAOJER-01 and CAMAQ-01 biotypes showed CYP450 metabolism mediating penoxsulam resistance in addition to the target site mutation. In conclusion, the mutations Ala122Thr, Ala205Asn, Trp574Leu, and Ser653Asn confer resistance to imazethapyr, but only Trp574Leu confers resistance to the other chemical groups. The herbicides penoxsulam, bispyribac-sodium, and nicosulfuron are effective in controlling three out of four mutations. CYP450-mediated metabolism coexists in biotypes carrying the Trp574Leu mutation. The subgenome location of the <i>ALS</i> mutation may result in variable levels of resistance.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 ","pages":"e70168"},"PeriodicalIF":2.3,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13099262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147779139","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":"PLDC-Net: A Domain-Specific Base Model for Plant Leaf Disease Classification Domain Adaptation Tasks.","authors":"David J Richter, Kyungbaek Kim","doi":"10.1002/pld3.70167","DOIUrl":"10.1002/pld3.70167","url":null,"abstract":"<p><p>Plant diseases are the cause of heavy losses of crop production and, therefore, a big contributor to food shortages. Identifying these diseases as early as possible is important to limit the negative effects that these diseases have on the yields, as slow response time will lead to the spread of diseases and further loss. Traditionally, trained staff will go into the fields, multiple times during the growth period, and inspect the plants in samples through field disease monitoring. These traditional processes are time-consuming and costly, and can be error-prone, if the staff is not properly educated or if the staff simply makes mistakes due to oversight, for example. To aid farmers with the process of correctly identifying diseases, artificial intelligence deep learning methods have been employed in recent years. However, to train such deep learning models, one needs to obtain sufficiently large and high-quality datasets and a model architecture that is capable of extracting relevant features to accurately classify the plant leaves. Datasets are still a limitation in the field of plant leaf disease classification. As such, domain adaptation methods such as transfer learning are often employed to overcome this data shortage. However, in current research, these domain adaptation methods almost exclusively rely on ImageNet as the pretraining dataset, a dataset that is domain unrelated to plant leaf disease detection, and models are often left unmodified and un-optimized as a result. In this work, we propose the pretraining of an improved attention-based and SiLU-activated DenseNet201 architecture called PLDC-Net that is pretrained on a large-scale plant leaf disease dataset constructed by the authors to create a domain-specific base model for better domain adaptation to new plants and diseases, validating the improved results through transfer learning, fine-tuning, one-shot learning, and few-shot learning. PLDC-Net has managed up to just over 24% improvements in F1-Score over the baseline in domain adaptation results.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 4","pages":"e70167"},"PeriodicalIF":2.3,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13088867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147723646","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":"Integrated Metabolomics, Transcriptomics, and Ultrastructural Assessment of the Myco-Heterotrophic Plant, <i>Monotropa uniflora</i>.","authors":"Sara Hazinia, Rezwan Tanvir, Yubo Wang, Zongyi Sun, Lei Wang, Fanbo Meng, Xiyin Wang, Ling Li, Basil J Nikolau","doi":"10.1002/pld3.70165","DOIUrl":"10.1002/pld3.70165","url":null,"abstract":"<p><p>A systems biology approach was used to characterize <i>Monotropa uniflora</i>, a nonhotosynthetic, myco-heterotrophic plant. In contrast to autotrophic plants, myco-heterotrophic plants obtain carbon and other nutrients by connecting roots to fungi, which establish the physical connection to a photosynthetic host, and thereby source required nutrients. Although a large proportion of plants form mycorrhizal associations, heterotrophic plants that are completely dependent on the mycorrhizal association for nutrients are rare and less well studied. The potential of developing <i>M. uniflora</i> as a model for myco-heterotrophic plants is demonstrated by datasets collected within this study, which include cellular ultrastructural morphologies, metabolomes and transcriptomes from tissue-types that are at different stages of growth or development. The morphological comparisons indicate that cells of the lower stem are older than those of the upper stem. The molecular -omics datasets reveal greater differences as the result of development rather than growth. Despite the obvious absence of photosynthetic functions in <i>M. uniflora</i>, as in photosynthetic plants the most abundant metabolites are sugars and organic acids that are used to translocate carbon in the latter. KEGG pathway enrichment analysis of the transcriptomes indicates that catabolic processes are highly active, which is consistent with the hypothesis that these processes generate intermediary energy metabolites (i.e., ATP and NAD(P)H) that can support anabolic processes associated with growth or development. Correlative analyses of the abundance of cutin monomers or cuticular waxes relative to the expressed transcriptomes identified co-expressing genes, revealing coordinated lipid metabolism network(s) that support cuticle formation in the absence of photosynthetic energy production. This model systems biology study of a myco-heterotrophic plant offers baseline insights into the functioning and resilience of ecological niches that are increasingly threatened by anthropogenic pressures.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 4","pages":"e70165"},"PeriodicalIF":2.3,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13084197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147723603","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":"A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants.","authors":"Benjamin E Haas, Faaiza Saif, Emily Bolger, Lynn Doran, Emma Rosales, Abigail Kim, Steven J Burgess, Stephen P Long","doi":"10.1002/pld3.70163","DOIUrl":"10.1002/pld3.70163","url":null,"abstract":"<p><p>Upstream open reading frames (uORFs) are regulatory elements present in the 5' leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome-wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild-type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost-efficient alternative to investigate transcript leaders by co-expression of two fluorescent proteins in <i>Nicotiana benthamiana</i> leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO₂ assimilation during sun-shade transitions.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 4","pages":"e70163"},"PeriodicalIF":2.3,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13084149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147723633","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":"FIMBRIN2 Regulates ABA-Induced Stomatal Closure by Promoting Microfilament Bundling and Turnover in Arabidopsis Guard Cells.","authors":"Zixuan Wang, Yuchong Han, Pan Wang, Pengfang Sun, Miao Hu, Rong Yu","doi":"10.1002/pld3.70162","DOIUrl":"https://doi.org/10.1002/pld3.70162","url":null,"abstract":"<p><p>In terrestrial plants, drought stress activates abscisic acid (ABA) signaling in guard cells, prompting stomatal closure to reduce water loss. Stomatal closure is accompanied by reorganization of the microfilaments. However, the mechanism by which ABA signaling regulates microfilaments disassembly remains unclear, and the actin-binding proteins (ABPs) involved in this process have yet to be fully identified. In this study, we demonstrated that FIMBRIN2 (FIM2), an actin-bundling protein, has its expression in guard cells upregulated by ABA, and FIM2 is involved in ABA-induced stomatal closure. The <i>fim2</i> mutant exhibits a drought-sensitive phenotype and delayed stomatal closure. Further confocal microscopy observations confirmed that this delay results from impaired actin bundling and reduced actin turnover activity. These findings reveal FIM2's role in ABA-induced stomatal closure and deepen our understanding of the functions of ABPs and the actin cytoskeleton in plant stress adaptation.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 4","pages":"e70162"},"PeriodicalIF":2.3,"publicationDate":"2026-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13071139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147691823","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":"Detection and Quantification of Dysprosium in Plant Tissues.","authors":"Edmaritz Hernández-Pagán, Kanjana Laosuntisuk, Alex T Harris, Allison N Haynes, David Buitrago, Anisa Guedira, Cyprian Rajabu, Michael W Kudenov, Colleen J Doherty","doi":"10.1002/pld3.70164","DOIUrl":"https://doi.org/10.1002/pld3.70164","url":null,"abstract":"<p><p>The growing demand for rare-earth elements (REEs), particularly dysprosium (Dy), underscores the need for sustainable extraction methods. Recovery of Dy, particularly from geographically distributed waste sources, is challenging. This gap positions phytomining, a technique using plants to accumulate metals, as a promising alternative. However, plant species differ in their ability to accumulate metals in high concentrations, necessitating efficient screening methods. In this study, we developed a high-throughput fluorescence-based assay to detect and quantify Dy uptake in plant tissues. The Dy detection method described in the present work exploits Dy's unique spectroscopic properties for sensitive and efficient analysis, enabling the detection of concentrations as low as 0.07 μM, with a detection limit of 0.2 μM in a plant matrix. By incorporating sodium tungstate (Na₂WO₄) as a fluorescence enhancer, we achieved robust emission intensities at 480 and 580 nm, facilitating Dy quantification in complex plant matrices. Additionally, the use of time-resolved fluorescence techniques reduces background autofluorescence from plant tissues, enhancing signal specificity. Validation of the fluorescence method with inductively coupled plasma mass spectrometry (ICP-MS) demonstrated a strong correlation in Dy levels. Greenhouse trials confirmed the method's utility for screening Dy accumulation in living plants and highlighted the potential for rapid stand-off detection. This fluorescence-based approach offers a scalable, efficient tool for identifying Dy-accumulating plants and advances phytomining as a sustainable strategy for REE recovery.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 4","pages":"e70164"},"PeriodicalIF":2.3,"publicationDate":"2026-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13070872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147691815","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":"Genome-Wide Identification of MYB Genes and Analysis of Their Expression Under Cold Stress Conditions in <i>Artocarpus heterophyllus</i>.","authors":"Xiangwei Ma, Pengjin Zhu, Weiyan Ye, Chenxin Yi, Xiuguan Tang, Jianjun Liang, Zhuangmin Wei, Qiqi Song, Hailan Zhou, Shengli Tang","doi":"10.1002/pld3.70131","DOIUrl":"https://doi.org/10.1002/pld3.70131","url":null,"abstract":"<p><p>Jackfruit (<i>Artocarpus heterophyllus</i>) thrives in subtropical and tropical areas but is vulnerable to winter cold stress. The myeloblastosis (MYB) transcription factor family plays an important role in plant biological and abiotic stress responses; however, their response to regional cold injury in jackfruit remains unexplored. The study aimed to identify and analyze the expression of 298 MYB genes in jackfruit under cold stress conditions. The study used genome-wide identification, bioinformatics analysis, and qPCR to analyze the expression of 298 MYB genes in jackfruit under cold stress. Evolutionary tree analysis showed that the AhMYB family members were divided into seven subfamilies. Chromosome mapping results showed that 298 AhMYB family members were unevenly distributed on 27 chromosomes. In addition, analysis of conserved motifs and gene structure showed that members of the AhMYB family located in the same subfamily had similar conserved motifs and gene structure. Collinear analysis identified 1439 duplicated fragments involving AhMYB family members within the species. In addition, the <i>cis</i>-acting elements in the promoters of AhMYB family members are implicated in many aspects of plant growth and development. Transcriptomic analysis of jackfruit under low-temperature stress showed that the expression patterns of AhMYB family members differed in jackfruit varieties. qPCR analysis further verified this result, confirming that AhMYB family members are involved in the response to low-temperature stress in jackfruit varieties. These findings provide new insights into the functions of AhMYB family members.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 4","pages":"e70131"},"PeriodicalIF":2.3,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13067916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147675898","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":"CUT&Tag for High-Resolution Epigenomic Profiling From a Low Amount of <i>Arabidopsis</i> Tissue.","authors":"Yixuan Fu, Marc W Schmid, Sara Simonini","doi":"10.1002/pld3.70161","DOIUrl":"https://doi.org/10.1002/pld3.70161","url":null,"abstract":"<p><strong>Background: </strong>The genome-wide profiling of chromatin states that are defined by different histone posttranslational modifications, known as epigenomic profiling, is crucial for understanding the epigenetic regulations of gene expression, both in animal and plant systems. CUT&Tag (Cleavage Under Targets and Tagmentation) is a novel enzyme-tethering method for epigenomic profiling, initially developed for mammalian cells. CUT&Tag has several advantages compared to the most commonly used epigenomic profiling methods such as chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). CUT&Tag allows epigenenomic profiling from a much smaller amount of starting material compared to ChIP-seq. Moreover, CUT&Tag relies on in situ DNA cleavage mediated by a transposase tethered to antibodies, while ChIP-seq typically involves nearly random DNA fragmentation. This fundamental difference raises the important question of whether CUT&Tag provides distinct advantages in terms of resolution and the precision of epigenomic profiles compared to ChIP-seq.</p><p><strong>Results: </strong>We profiled the genome-wide distribution of three histone modifications, H3K27me3, H3K4me3, and H3K27Ac, from a few seedlings of <i>Arabidopsis</i> that weighed around 0.01 g. We compared the CUT&Tag H3K27me3 profile with publicly available H3K27me3 profiles generated from ChIP-seq, and ChIPmentation, a ChIP-seq-based technique where MNase and Tn5 transposon are used to cleave the chromatin and prepare sequencing libraries, respectively. We showed that all these techniques capture the same broad lines of the epigenomes, but they also showed preferences toward different genomic features and revealed different sets of peaks. Analysis using the CUT&Tag datasets for the three histone modifications revealed their genomic locations and their relationship with the gene expression level, which are consistent with the expected effect of these histone marks on gene transcription. By comparing to the nucleosome occupancy data, we show that CUT&Tag reached resolution at the single-nucleosome level, which is similar to that of ChIPmentation, but higher than that of ChIP-seq. Moreover, both CUT&Tag and ChIPmentation data revealed an enrichment of H3K27me3 mark on exons, thus providing a deeper understanding of epigenome features that could not be resolved by ChIP-seq.</p><p><strong>Conclusion: </strong>CUT&Tag is a valid, easy-to-perform, cost-effective, and reliable approach for efficient epigenomic profiling in <i>Arabidopsis</i>, compatible with limited amounts of plant tissue, and provides a higher resolution compared to that of ChIP-seq. Because the CUT&Tag protocol starting input is isolated nuclei, it is applicable to model and nonmodel plants.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"10 4","pages":"e70161"},"PeriodicalIF":2.3,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13067811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147675931","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}