Plant Communications最新文献

{"title":"A long terminal repeat retrotransposon in the OsACS6 promoter enhances the epigenetic regulation of lysophospholipid contents in rice grains.","authors":"Kang Li, Yan Cheng, Jingyao Yu, Lanjun Luo, Ling Liu, Luis Alejandro José Mur, Jie Luo, Chuanying Fang","doi":"10.1016/j.xplc.2025.101375","DOIUrl":"10.1016/j.xplc.2025.101375","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101375"},"PeriodicalIF":11.6,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12365819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GPS: Harnessing data fusion strategies to improve the accuracy of machine learning-based genomic and phenotypic selection.","authors":"Hongshan Wu, Shichao Jin, Chao Xiang, Jianling Tang, Junhong Xian, Jiaoping Zhang, Jinming Zhao, Xianzhong Feng, Dong Jiang, Yufeng Wu, Yanfeng Ding","doi":"10.1016/j.xplc.2025.101416","DOIUrl":"10.1016/j.xplc.2025.101416","url":null,"abstract":"<p><p>Genomic selection (GS) and phenotypic selection (PS) are widely used for accelerating plant breeding. However, the accuracy, robustness, and transferability of these two selection methods are underexplored, especially when addressing complex traits. In this study, we introduce a novel data fusion framework, GPS (genomic and phenotypic selection), designed to enhance predictive performance by integrating genomic and phenotypic data through three distinct fusion strategies: data fusion, feature fusion, and result fusion. The GPS framework was rigorously tested using an extensive suite of models, including statistical approaches (GBLUP and BayesB), machine learning models (Lasso, RF, SVM, XGBoost, and LightGBM), a deep learning method (DNNGP), and a recent phenotype-assisted prediction model (MAK). These models were applied to large datasets from four crop species, maize, soybean, rice, and wheat, demonstrating the versatility and robustness of the framework. Our results indicated that: (1) data fusion achieved the highest accuracy compared with the feature fusion and result fusion strategies. The top-performing data fusion model (Lasso_D) improved the selection accuracy by 53.4% compared to the best GS model (LightGBM) and by 18.7% compared to the best PS model (Lasso). (2) Lasso_D exhibited exceptional robustness, achieving high predictive accuracy even with a sample size as small as 200 and demonstrating resilience to single-nucleotide polymorphism (SNP) density variations, underscoring its adaptability to diverse data conditions. Moreover, the model's accuracy improved with the number of auxiliary traits and their correlation strength with target traits, further highlighting its adaptability to complex trait prediction. (3) Lasso_D demonstrated broad transferability, with substantial improvements in predictive accuracy when incorporating multi-environmental data. This enhancement resulted in only a 0.3% reduction in accuracy compared to predictions generated using data from the same environment, affirming the model's reliability in cross-environmental scenarios. This study provides groundbreaking insights, pushing the boundaries of predictive accuracy, robustness, and transferability in trait prediction. These findings represent a significant contribution to plant science, plant breeding, and the broader interdisciplinary fields of statistics and artificial intelligence.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101416"},"PeriodicalIF":11.6,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12365829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A chromosome-level genome assembly for Ficus carica provides genetic insights into flowerless fig fruit development, psoralen biosynthesis, and drought tolerance.","authors":"Shixiong Ren, Xun Gu, Zixi Chen, Yixin Liu, Xiya Zhao, Yawen Wang, Jinkai Lu, Jiawen Cui, Yanhui Si, Yonghua Zhang, Biao Jin, Qingjie Wang, Zhaogeng Lu, Li Wang","doi":"10.1016/j.xplc.2025.101470","DOIUrl":"10.1016/j.xplc.2025.101470","url":null,"abstract":"<p><p>Ficus carica L., an ancient crop of considerable economic value, exhibits distinctive biological traits, including flowerless fruit (syconium) development, psoralen biosynthesis, and drought tolerance. In this study, we present a chromosome-level genome assembly (323.03 Mb, N50 = 23.82 Mb) of F. carica, revealing an evolutionary divergence from the closely related genus Broussonetia approximately 50 million years ago. Comparative genomic analyses revealed a contraction in the s-domain receptor-like kinase gene family, which is associated with unisexual fruit formation, and identified conserved MADS-box transcription factor genes (FcAGL6, FcAP2, and FcSEP1/2) that regulate syconium development through spatiotemporal expression patterns. Metabolomic profiling demonstrated tissue-specific accumulation of bioactive compounds, with roots serving as the primary reservoir for psoralen. We also identified key genes-FcANS and FcCHS10, involved in anthocyanin biosynthesis, and FcMS, involved in psoralen biosynthesis-and validated their functions using a newly established transient transformation system. Transcriptomic analysis under drought stress identified the NAC transcription factor FcJA2 as a central regulator of stress tolerance that enhances reactive oxygen species scavenging and osmotic regulation by activating FcPP2C5 and FcP5CS. Overexpression of FcJA2 significantly improved drought resistance. Further analyses demonstrated that FcJA2-mediated drought-response modules are conserved across the Moraceae. These findings provide valuable insights into the genetic mechanisms underlying fruit development, specialized metabolite biosynthesis, and stress tolerance in F. carica, offering potential applications for crop improvement and advancing our understanding of genome evolution and environmental adaptability in the Moraceae family.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101470"},"PeriodicalIF":11.6,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144796105","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":"Oligosaccharide elicitors in plant immunity: Molecular mechanisms and disease resistance strategies.","authors":"Guangzheng Sun, Yu Xiao, Heng Yin, Ke Yu, Yiming Wang, Yuanchao Wang","doi":"10.1016/j.xplc.2025.101469","DOIUrl":"10.1016/j.xplc.2025.101469","url":null,"abstract":"<p><p>The recognition of oligosaccharide elicitors, which originate from both pathogens and hosts, by membrane-localized receptors is of fundamental importance for triggering host immunity and disease resistance. It is therefore a topic of utmost significance for agricultural and botanical research. This review provides a comprehensive analysis of our current understanding of the types of oligosaccharide elicitors. We explore their diverse immunological functions, aiming to uncover the underlying mechanisms. We then detail the known recognition receptors for these oligosaccharide elicitors and describe the immune signaling pathways in which they participate. We outline the counter-defense strategies used by pathogens in response to oligosaccharide-induced immunity, offering insight into the complex interactions between plants and pathogens. Finally, we discuss challenges and limitations in the field of oligosaccharide-based immunity and propose directions for future research. A holistic view of oligosaccharide elicitors can facilitate the development of more effective strategies for enhancing plant disease resistance by leveraging mechanisms of oligosaccharide-induced immunity, ultimately promoting more sustainable agricultural practices and a better understanding of plant-pathogen interactions.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101469"},"PeriodicalIF":11.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144776863","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":"Three PP2C phosphatases modulate FERONIA receptor kinase activity to regulate pollen-stigma interaction in Arabidopsis.","authors":"Lijun Cheng, Zhiwen Liu, Baiyan Lu, Sihan Gao, Junwei Zhao, Chao Li","doi":"10.1016/j.xplc.2025.101468","DOIUrl":"10.1016/j.xplc.2025.101468","url":null,"abstract":"<p><p>Pollen hydration represents the initial and critical step in pollen-stigma interactions and is necessary for successful plant fertilization. The FERONIA (FER) receptor kinase regulates pollen hydration by modulating stigmatic reactive oxygen species (ROS) accumulation through rapid alkalinization factor 23/33 (RALF23/33) and pollen coat protein B-class peptide (PCP-B) signaling. However, the function and regulatory mechanism of FER's receptor kinase activity in pollen hydration remain poorly understood. In this study, we found that the kinase-dead form of FER^K565R fails to restore stigmatic ROS accumulation and pollen hydration in the fer-4 mutant. By integrating RNA sequencing database analyses with yeast two-hybrid assays, we identified three type 2C phosphatases (PP2Cs)-protein phosphatase 2C clade H 1 (PP2CH1) and clade-E Growth-Regulating 1 and 2 (EGR1 and EGR2)-that interact with FER at the plasma membrane. These PP2Cs dephosphorylate FER at Ser695 and Thr696 within the activation segment, thereby inhibiting its kinase activity. Mutations at these two residues reduced ROS levels in the stigma and increased pollen hydration rates. Altogether, this study reveals a crucial regulatory mechanism of FER signaling, demonstrating that PP2CH1, EGR1, and EGR2 act as negative regulators of FER kinase activity to modulate stigmatic ROS accumulation and promote pollen hydration.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101468"},"PeriodicalIF":11.6,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762295","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":"Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.","authors":"Merijn Kerstens, Yvet Boele, Abraham Morales-Cruz, Chris Roelofsen, Peng Wang, Leo A Baumgart, Ronan O'Malley, Gabino Sanchez-Perez, Ben Scheres, Viola Willemsen","doi":"10.1016/j.xplc.2025.101466","DOIUrl":"10.1016/j.xplc.2025.101466","url":null,"abstract":"<p><p>Conserved non-coding sequences (CNSs) are integral elements of transcriptional regulation. Transcriptional tuning of PLETHORA (PLT) genes that encode master regulators of plant development is vital for embryogenesis and meristematic function. However, how the expression of PLT genes is modulated through CNSs remains unclear. Through motif-based mining of upstream sequences in 120 angiosperm genomes, we identified 21 conserved and lineage-specific CNSs, two of which are unusually long, similar, and colinear within eudicots. Using Arabidopsisthaliana, we demonstrate that these two deeply conserved elements, which we named BOX1 and BOX2, control PLT1 and PLT2 expression. CRISPR mutants within these elements specifically reduced PLT expression levels, and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip, affecting the ability to rescue the plt1 plt2 double mutant. We further show that the influence of these elements on expression patterns is already exerted during embryogenesis and functional in the context of the early embryo. Finally, we reveal the existence of a BOX-mediated autoregulatory feedback loop that, in large part, explains CNS influence on expression patterns. We thus uncover a transcriptional mechanism by which genes encoding master regulators of embryo and root meristem development are regulated.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101466"},"PeriodicalIF":11.6,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755106","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":"MPK6-mediated phosphorylation destabilizes MYC2 and attenuates its transcriptional activity in jasmonate signaling.","authors":"Jong Hee Im, Seungmin Son, Man-Young Jung, Jae-Heung Ko, Kyung-Hwan Han","doi":"10.1016/j.xplc.2025.101465","DOIUrl":"10.1016/j.xplc.2025.101465","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101465"},"PeriodicalIF":11.6,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719150","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":"Near-complete genome assembly of allotetraploid Erianthus rockii reveals unique chromosome evolution and lineage-divergence trajectories in the Saccharum complex.","authors":"Baiyu Wang, Zhe Zhang, Yiying Qi, Yuxuan Wei, Jing Mei, Hanjing Liu, Yuhao Wang, Yaxue Fang, Xiuting Hua, Hongyan Ding, Yixing Zhang, Xiaoxi Feng, Yumin Huang, Zhen Li, Hailong Chang, Qinnan Wang, Xiuqin Lin, Xinlong Liu, Zuhu Deng, Wei Yao, Haibao Tang, Jisen Zhang","doi":"10.1016/j.xplc.2025.101464","DOIUrl":"10.1016/j.xplc.2025.101464","url":null,"abstract":"<p><p>The Saccharum complex is known for having one of the most intricate genomes among plants, primarily originating from autopolyploidization. Erianthus rockii (E. rockii), an allotetraploid species within the Saccharum complex, serves as a key phylogenetic reference for studying polyploidization in Saccharum. Here, we present the gap-closed genome of E. rockii and investigate the origin and evolution of the Saccharum complex. The Saccharum complex species are thought to have originated from chromosome fusion and polyploidization events that trace back to a diploid common ancestor, approximately 5.1 million years ago. Comparative genomics analyses reveal the driving forces behind the rapid mobility of centromeres, as well as the fates of multiple centromeres after chromosome fusion events. Differences in transposable elements and DNA methylation, structural variations, reorganizations in three-dimensional chromatin architecture, and expression biases offer insights into the concerted diploidization process and the interplay between the A and B sub-genomes of E. rockii. Population genetics and spatiotemporal distribution data suggest that Saccharum lineages originated in the pan-Himalayan regions from a diploid last common ancestor. Dynamic processes such as chromosome reduction, autopolyploidization, and allopolyploidization, likely driven by climate change, contributed to the spread and emergence of the Saccharum lineage. Our findings highlight the evolution of polyploid genomes and provide a fundamental genetic resource for the breeding and genetic improvement of sugarcane.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101464"},"PeriodicalIF":11.6,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719151","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":"Complete genome assembly of japonica rice variety Zhonghua 11.","authors":"Xue-Feng Yao, Zongyi Sun, Xintong Xu, Huihui Li, Chun-Ming Liu","doi":"10.1016/j.xplc.2025.101463","DOIUrl":"10.1016/j.xplc.2025.101463","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101463"},"PeriodicalIF":11.6,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700331","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 biosynthesis and diversity of taxanes: From pathway elucidation to engineering and synthetic biology.","authors":"Jingcheng Shi, Caibin Zhang, Rui Deng, Alisdair R Fernie, Moxian Chen, Youjun Zhang","doi":"10.1016/j.xplc.2025.101460","DOIUrl":"10.1016/j.xplc.2025.101460","url":null,"abstract":"<p><p>Taxanes are diterpenoid natural products found in yew trees (Taxus spp.) and include three anticancer agents: paclitaxel, docetaxel, and cabazitaxel. Despite nearly 500 reported taxane compounds, only the biosynthetic pathway of the type I taxane skeleton leading to paclitaxel is close to being fully elucidated. Traditional extraction of these compounds is unsustainable, and chemical synthesis is commercially nonviable. With emerging drug resistance and limited compound diversity, there is a critical need to expand the taxane library and develop sustainable production methods. Here, we propose strategies to elucidate the biosynthetic pathways of various taxane skeletons by identifying and engineering key enzymes such as diterpene synthases, cytochrome P450s (CYP450s), acetyltransferases, and BAHD acyltransferases (BEAT, AHCT, HCBT, and DAT). We examine the roles of metabolon-forming enzyme complexes in optimizing metabolic flux and highlight the use of plant chassis such as Nicotiana benthamiana or microbial chassis such as Escherichia coli and Saccharomyces cerevisiae for sustainable taxane biosynthesis. Techniques such as compartmentalization and CRISPRi-dCas9-based gene circuits are discussed as means to enhance production efficiency. Additionally, artificial intelligence (AI)-guided directed evolution of CYP450s is proposed as a strategy to engineer enzymes with desired properties, facilitating the production of novel and new-to-nature taxane derivatives. The integration of these approaches would support the development of a comprehensive taxane library, which could accelerate the discovery of new therapeutic agents.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101460"},"PeriodicalIF":11.6,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692313","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}