Plant Molecular Biology最新文献

{"title":"Retraction Note: A novel approach for developing resistance in rice against phloem limited viruses by antagonizing the phloem feeding hemipteran vectors.","authors":"Prasenjit Saha, Indranil Dasgupta, Sampa Das","doi":"10.1007/s11103-025-01633-2","DOIUrl":"10.1007/s11103-025-01633-2","url":null,"abstract":"","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"103"},"PeriodicalIF":3.8,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144795085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TISCalling: leveraging machine learning to identify translational initiation sites in plants and viruses.","authors":"Ming-Ren Yen, Ya-Ru Li, Chia-Yi Cheng, Ting-Ying Wu, Ming-Jung Liu","doi":"10.1007/s11103-025-01632-3","DOIUrl":"10.1007/s11103-025-01632-3","url":null,"abstract":"<p><p>The recognition of translational initiation sites (TISs) offers complementary insights into identifying genes encoding novel proteins or small peptides. Conventional computational methods primarily identify Ribo-seq-supported TISs and lack the capacity of systematic and global identification of TIS, especially for non-AUG sites in plants. Additionally, these methods are often unsuitable for evaluating the importance of mRNA sequence features for TIS determination. In this study, we present TISCalling, a robust framework that combines machine learning (ML) models and statistical analysis to identify and rank novel TISs across eukaryotes. TISCalling generalized and ranks important features common to multiple plant and mammalian species while identifying kingdom-specific features such as mRNA secondary structures and \"G\"-nucleotide contents. Furthermore, TISCalling achieved high predictive power for identifying novel viral TISs. Importantly, TISCalling provides prediction scores for putative TIS along plant transcripts, enabling prioritization of those of interest for further validation. We offer TISCalling as a command-line-based package [ https://github.com/yenmr/TISCalling ], capable of generating prediction models and identifying key sequence features. Additionally, we provide web tools [ https://predict.southerngenomics.org/TISCalling/ ] for visualizing pre-computed potential TISs, making it accessible to users without programming experience. The TISCalling framework offers a sequence-aware and interpretable approach for decoding genome sequences and exploring functional proteins in plants and viruses.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"102"},"PeriodicalIF":3.8,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12316744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Superior thermostability and divalent cation sensitivity of isoamylase CMI294C from Cyanidioschyzon merolae.","authors":"Keisuke Okada, Taichi Someya, Takashi Osanai","doi":"10.1007/s11103-025-01623-4","DOIUrl":"10.1007/s11103-025-01623-4","url":null,"abstract":"<p><p>A storage polysaccharide in the red alga Cyanidioschyzon merolae is semi-amylopectin, a glucan with properties intermediate between noncrystalline glycogen and semicrystalline amylopectin. The debranching enzyme isoamylase plays a crucial role in determining the semicrystalline nature of glucans. In amylopectin-storing organisms, isoamylases consist of the isozymes ISA1, ISA2, and ISA3, with the former two primarily responsible for semicrystallinity. While the semicrystallinity of C. merolae semi-amylopectin is weaker than that of amylopectin, it retains a semicrystalline structure. Based on a previous analysis of isoamylase-deficient strains of C. merolae, the isoform CMI294C is the main contributor to glucan synthesis. Although the biochemical properties of isoamylases involved in amylopectin synthesis have been characterized, those of isoamylases involved in semi-amylopectin synthesis remain largely unknown. Here, we performed a detailed biochemical analysis of CMI294C to gain insights of isoamylases in semi-amylopectin synthesis. Similar to isoamylases in amylopectin-synthesizing organisms, CMI294C hydrolyzes amylopectin more efficiently than glycogen. However, unlike typical isoamylases, CMI294C is uniquely more active against pullulan than against glycogen; and it is strongly inhibited by Zn²⁺. Our results indicate that CMI294C can be potentially used for industrial maltose production due to its enzymatic properties. Overall, our findings provide molecular insights into the isoamylase in glucan structure modulation and enhance our understanding of glucan metabolism in C. merolae.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"99"},"PeriodicalIF":3.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12313807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TcJAMYC5 positively regulates paclitaxel biosynthesis in Taxus chinensis var. Mairei.","authors":"Shiyu Cai, Lina Xue, Ziling Tao, Fengxiu Li, Qiao Liu, Wen Wan, Jihong Jiang, Ludan Li, Xiaoying Cao","doi":"10.1007/s11103-025-01626-1","DOIUrl":"10.1007/s11103-025-01626-1","url":null,"abstract":"<p><p>Paclitaxel is an important natural anticancer drug. Its biosynthesis is very complex and 18 enzymes likely involved have been characterized. However, the regulatory mechanism of these enzyme genes still remains to be elucidated. Here we identified a novel transcription factor in the MYC family of Taxus chinensis TcJAMYC5 function in paclitaxel biosynthesis. TcJAMYC5 was highly expressed in the roots and regulated by MeJA. Transient overexpression of TcJAMYC5 in T. chinensis cambial meristematic cells resulted in a significant increase in paclitaxel and bacctin III content and upregulated expression of nearly all of paclitaxel biosynthesis related genes except T13αOH. Suppression of TcJAMYC5 expression in cambial meristematic cells resulted in a significant decrease in paclitaxel content. TcJAMYC5 could bind to promoters of paclitaxel biosynthesis pathway enzyme genes TASY, DBTNBT and T5αH for directly activating their expression. Taken together, we conclude that TcJAMYC5 is an activator that improves the accumulation of paclitaxel in T. chinensis through a MeJA-medicated signaling pathway.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"97"},"PeriodicalIF":3.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chickpea (Cicer arietinum L.) battling against heat stress: plant breeding and genomics advances.","authors":"Uday Chand Jha, Yogesh Dashrath Naik, Manu Priya, Harsh Nayyar, Parvaze A Sofi, Radha Beena, Himabindu Kudapa, Kousik Atta, Mahendar Thudi, P V Vara Prasad, Kadambot H M Siddique","doi":"10.1007/s11103-025-01628-z","DOIUrl":"10.1007/s11103-025-01628-z","url":null,"abstract":"<p><p>Global climate change, particularly the increasing frequency and intensity of heat stress, poses a significant threat to crop productivity. Chickpea (Cicer arietinum L.) employs various physiological, biochemical, and molecular mechanisms to cope with elevated temperatures, including maintaining leaf chlorophyll content to preserve the functional integrity of photosystem II (PSII) and enhancing canopy temperature depression to reduce overheating. These traits are crucial for sustaining photosynthetic efficiency, plant health, and yield stability under heat stress. Recent advances in multi-omics approaches-including genomics, transcriptomics, proteomics, and metabolomics-have enhanced our understanding of the genetic basis of heat stress tolerance in chickpea. These tools have facilitated the identification of key genes and molecular pathways involved in heat stress responses. Functional characterization of these genes has provided insights into their roles within the complex metabolic and signaling networks that underpin heat resilience. This review explores integrating conventional and modern breeding technologies with high-throughput phenotyping (HTP) platforms to accelerate genetic gains in chickpea under heat stress. HTP tools enable rapid, precise screening of heat-resilient traits, facilitating early selection of superior genotypes. We also highlight recent genomic advancements, including genome-wide association studies, whole-genome resequencing, and pangenome assemblies, which have uncovered novel structural variants, candidate genes, and haplotypes associated with heat tolerance. Leveraging these resources in conjunction with functional analyses offers new opportunities for breeding climate-resilient chickpea cultivars capable of delivering stable yields and quality under adverse conditions. These developments are crucial for safeguarding chickpea productivity and ensuring global food and nutrition security amid climate change.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"101"},"PeriodicalIF":3.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling transcriptional regulation underpinning chilling and frost stress response in Trans-Himalayan Hippophae tibetana L.","authors":"Romit Seth, Amna Devi, Phuntsog Dolkar, Rajni Parmar, Shikha Sharma, Balraj Sharma, Praveen Dhyani, Tsering Stobdan, Ram Kumar Sharma","doi":"10.1007/s11103-025-01619-0","DOIUrl":"10.1007/s11103-025-01619-0","url":null,"abstract":"<p><p>Hippophae tibetana is an enigmatic least explored Seabuckthorn species, with exceptional adaptability to sub-zero temperatures in Trans-Himalayan region. This study integrates physiological and transcriptional profiling to understand its unique cold stress resilience. The physiological assessment including chlorophyll content, relative water content, and electrolyte leakage were least affected during the early response (ER) of cold stress as compared to prolonged (PR) and freeze response (FR), which was effectively restored during the recovery phase (RR). Genome-guided de novo assembly yielded 25,176 high-quality unigenes (N50: 2195 bp; BUSCO: 92.9%), with 75.9% functionally annotated using NCBI-nr, Araport11, SwissProt, COG, KEGG, and Pfam databases. Clustering of differentially expressed unigenes revealed ER (4467 DEGs) and RR (4478) grouped distinctly from PR (14,150) and FR (14,528), underscoring significantly heightened transcriptional reprogramming during PR/FR compared to ER/RR. Furthermore, the integration of transcriptional interactome network with GO and KEGG enrichment highlighted ICE1-CBF regulatory network with significant upregulation of Inducer of CBF Expression (ICE1), Cold receptive protein kinase (CRPK1), anti-freeze proteins (AFPs), and pathways like jasmonic acid signaling, carbohydrate metabolism, and membrane stabilization as key to cold tolerance during PR and FR phases. The current study advances our understanding of cold stress resilience in H. tibetana, elucidating its adaptive mechanisms in extreme Trans-Himalayan environments. The comprehensive genomic resources and key candidates identified here may provide a foundation for discovering cold tolerance-associated genome-wide variations in priority crops and plantation species.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"96"},"PeriodicalIF":3.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An explainable vision transformer with transfer learning based efficient drought stress identification.","authors":"Aswini Kumar Patra, Ankit Varshney, Lingaraj Sahoo","doi":"10.1007/s11103-025-01620-7","DOIUrl":"10.1007/s11103-025-01620-7","url":null,"abstract":"<p><p>Early detection of drought stress is critical for taking timely measures for reducing crop loss before the drought impact becomes irreversible. The subtle phenotypical and physiological changes in response to drought stress are captured by non-invasive imaging techniques and these imaging data serve as valuable resource for machine learning methods to identify drought stress. While convolutional neural networks are in wide use, vision transformers (ViTs) present a promising alternative in capturing long-range dependencies and intricate spatial relationships, thereby enhancing the detection of subtle indicators of drought stress. We propose an explainable deep learning pipeline that leverages the power of ViTs for drought stress detection in potato crops using aerial imagery. We applied two distinct approaches: a synergistic combination of ViT and support vector machine (SVM), where ViT extracts intricate spatial features from aerial images, and SVM classifies the crops as stressed or healthy and an end-to-end approach using a dedicated classification layer within ViT to directly detect drought stress. Our key findings explain the ViT model's decision-making process by visualizing attention maps. These maps highlight the specific spatial features within the aerial images that the ViT model focuses as the drought stress signature. Our findings demonstrate that the proposed methods not only achieve high accuracy in drought stress identification but also shedding light on the diverse subtle plant features associated with drought stress. This offers a robust and interpretable solution for drought stress monitoring for farmers to undertake informed decisions for improved crop management.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"98"},"PeriodicalIF":3.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: DUO1 Activated Zinc Finger (AtDAZ) protein role in the generative cell body morphogenesis.","authors":"Abdur Rauf, Anbang Wang, Yujia Li, Zhihao Lian, Shouxing Wei, Qayash Khan, Kashmala Jabbar, Farooq Jan, Ikramullah Khan, Mamoona Bibi, Syed Abidullah, Jingyang Li","doi":"10.1007/s11103-025-01613-6","DOIUrl":"10.1007/s11103-025-01613-6","url":null,"abstract":"","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"95"},"PeriodicalIF":3.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144754030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic language models with k-mer tokenization strategies for plant genome annotation and regulatory element strength prediction.","authors":"Shosuke Suzuki, Kazumasa Horie, Toshiyuki Amagasa, Naoya Fukuda","doi":"10.1007/s11103-025-01604-7","DOIUrl":"10.1007/s11103-025-01604-7","url":null,"abstract":"<p><p>Recent advances in genomic language models have improved the accuracy of in silico analyses, yet many rely on resource-intensive architectures. In this study, we focus on the impact of k-mer tokenization strategies-specifically varying window sizes (three to eight) and overlap schemes-on the performance of transformer-based genomic language models. Through extensive evaluation across multiple plant genomic tasks, including splice site and alternative polyadenylation site prediction, we show that thoughtful design of the k-mer tokenizer plays a critical role in model performance, often outweighing model scale. In particular, overlap-based tokenization generally enhances performance by preserving local sequence context, while certain non-overlap configurations achieve competitive accuracy with improved computational efficiency in some tasks. Despite using a smaller model, our approach performs on par with the state-of-the-art AgroNT model in many cases. These results emphasize that k-mer tokenization, not merely model size, is a key determinant of success in genomic sequence modeling. Our findings provide practical guidance for designing efficient genomic language models tailored to plant biology.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"100"},"PeriodicalIF":3.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12313756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"To grow or not to grow: the enigma of plant root growth dynamism.","authors":"Drishti Mandal, Saptarshi Datta, Sicon Mitra, Swarnavo Chakraborty, Ronita Nag Chaudhuri","doi":"10.1007/s11103-025-01631-4","DOIUrl":"10.1007/s11103-025-01631-4","url":null,"abstract":"<p><p>Root growth and modulation in plants is a highly dynamic yet strictly regulated process. Primary root development in Arabidopsis for example, is an intricate balance between cell division in the meristematic zone and cell elongation in the elongation zone, followed by subsequent differentiation. This process involves an orchestrated series of events that depend on environmental and developmental cues. Regulation is imparted by a complex network of hormone signaling primarily involving auxin, in crosstalk with cytokinin, abscisic acid, jasmonic acid, ethylene and others. In course of evolution, plants have developed an incredible array of mechanisms to address water scarcity, including modulation of root system architecture. During low to moderate water deficiency plants, adopt a \"searching-for-water\" strategy evoking growth-promoting responses. This is marked by elongation of the primary root for water exploration in deeper soil layers. However, during severe drought stress, plants resort to a \"stop growth\" strategy and restrict root growth, to conserve resources and energy for survival. The balance between these adaptive responses is critically regulated by key phytohormones which interact synergistically or antagonistically, to control root growth under varying levels of water shortage. Understanding these adaptation strategies as to how plants integrate environmental cues and associated hormone signaling to influence root growth generates a wide range of possibilities for agricultural innovation. This article aims to provide an overview of the mechanisms acquired by the root system at the morphological, physiological, and molecular levels, under optimum growth conditions and in response to varying degrees of water paucity.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 4","pages":"93"},"PeriodicalIF":3.8,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144744150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}