Pub Date : 2026-02-05DOI: 10.1016/j.plaphy.2026.111108
Zhengjie Ji , Huihui Liu , Tobias Pöhnl , Susanne Neugart
This study provides a direct comparison of UV-B radiation (0.5 kJ m−2 d−1) and low temperature (10/12 °C) on secondary metabolites and enzyme activities in kale and pak choi, assessing both carotenoids and phenolics and including Arabidopsis wild type and uvr8 mutant under identical conditions for mechanistic validation. UV-B induced rapid accumulation of lutein, β-carotene, chlorophyll a, chlorophyll b and kaempferol glycosides in kale, while in pak choi, long-term low temperature or UV-B treatments (3–5 days) triggered similar responses. Notably, combined stress triggered synergistic accumulation of specific phenolic compounds in both species. Low temperature increased antioxidant activity and UV-B enhanced the activities of phenylalanine ammonia-lyase and peroxidase in both species; however, the interactive effects differed between species. Arabidopsis validation demonstrated the regulatory role of the UVR8 photoreceptor in mediating antioxidant responses and secondary metabolism under UV-B and low temperature. Taken together, exposure to UV-B radiation and low temperature according to species-specific responses could be a biotechnological tool to optimize the accumulation of bioactive compounds in Brassica vegetables, especially effective for vertical farming approaches.
{"title":"Interaction of preharvest UV-B and low temperature on antioxidant secondary plant metabolites in Brassica vegetables: A species-specific comparison of kale and pak choi","authors":"Zhengjie Ji , Huihui Liu , Tobias Pöhnl , Susanne Neugart","doi":"10.1016/j.plaphy.2026.111108","DOIUrl":"10.1016/j.plaphy.2026.111108","url":null,"abstract":"<div><div>This study provides a direct comparison of UV-B radiation (0.5 kJ m<sup>−2</sup> d<sup>−1</sup>) and low temperature (10/12 °C) on secondary metabolites and enzyme activities in kale and pak choi, assessing both carotenoids and phenolics and including <em>Arabidopsis</em> wild type and <em>uvr8 mutant</em> under identical conditions for mechanistic validation. UV-B induced rapid accumulation of lutein, <em>β</em>-carotene, chlorophyll <em>a</em>, chlorophyll <em>b</em> and kaempferol glycosides in kale, while in pak choi, long-term low temperature or UV-B treatments (3–5 days) triggered similar responses. Notably, combined stress triggered synergistic accumulation of specific phenolic compounds in both species. Low temperature increased antioxidant activity and UV-B enhanced the activities of phenylalanine ammonia-lyase and peroxidase in both species; however, the interactive effects differed between species. <em>Arabidopsis</em> validation demonstrated the regulatory role of the UVR8 photoreceptor in mediating antioxidant responses and secondary metabolism under UV-B and low temperature. Taken together, exposure to UV-B radiation and low temperature according to species-specific responses could be a biotechnological tool to optimize the accumulation of bioactive compounds in <em>Brassica</em> vegetables, especially effective for vertical farming approaches.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111108"},"PeriodicalIF":5.7,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146181826","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}
Nitrogen (N) limitation significantly constrains crop growth, yield and quality. Developing crop varieties with high N deficiency tolerance represents a critical strategy for reducing N fertilizer application and promoting sustainable agriculture. Semi-wild soybean offers valuable genetic resources for the improvement of soybean varieties. Nevertheless, the mechanisms underlying N deficiency tolerance remain poorly understood. In this study, we employed a comprehensive analytical approach—including Pearson's correlation analysis, principal component analysis, subordinate function analysis, and cluster analysis—to evaluate the N starvation tolerance of 50 semi-wild soybean varieties. Shoot fresh weight, root-shoot ratio, SPAD2 value and leaf nitrate content were identified as key indicators for assessing N starvation tolerance. The variety V03 was identified as the most N starvation-tolerant. Comparative physiological analyses revealed that V03 enhances tolerance to N deficiency by optimizing root architecture and sustaining the activity of nitrogen metabolism enzymes—such as nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase (GOGAT)—in root and leaf tissues. Transcriptomic analysis indicated that V03 exhibits a broader transcriptional response (with more N Starvation-induced DEGs) and functional reprogramming in root tissues, showing stronger enrichment in stress-responsive processes, regulatory functions, and plasma membrane-related terms as well as environmental information processing pathways. Furthermore, V03 displayed more pronounced changes in the expression of genes related to N transport, N assimilation and transcription factor (TF) compared to the N starvation-sensitive variety V46. This study provides a robust and comprehensive methodology for evaluating N deficiency tolerance in semi-wild soybean. Our findings offer new insights into the physiological adaptions and molecular regulatory network governing N uptake and metabolism, which may support future breeding efforts aimed at enhancing NUE in leguminous crops.
{"title":"Comprehensive evaluation, morpho-physiological and transcriptional response involving the tolerance of Semi-wild soybean (Glycine gracilis) seedlings to nitrogen starvation","authors":"Siqi Hou , Shixi Lu , Yuechuan Hou , Chunxiao Yu , Jiarui Zhang , Jichao Li , Chunmei Zong , Shuzhen Zhang , Xiaodong Ding , Jialei Xiao , Qiang Li","doi":"10.1016/j.plaphy.2026.111120","DOIUrl":"10.1016/j.plaphy.2026.111120","url":null,"abstract":"<div><div>Nitrogen (N) limitation significantly constrains crop growth, yield and quality. Developing crop varieties with high N deficiency tolerance represents a critical strategy for reducing N fertilizer application and promoting sustainable agriculture. Semi-wild soybean offers valuable genetic resources for the improvement of soybean varieties. Nevertheless, the mechanisms underlying N deficiency tolerance remain poorly understood. In this study, we employed a comprehensive analytical approach—including Pearson's correlation analysis, principal component analysis, subordinate function analysis, and cluster analysis—to evaluate the N starvation tolerance of 50 semi-wild soybean varieties. Shoot fresh weight, root-shoot ratio, SPAD2 value and leaf nitrate content were identified as key indicators for assessing N starvation tolerance. The variety V03 was identified as the most N starvation-tolerant. Comparative physiological analyses revealed that V03 enhances tolerance to N deficiency by optimizing root architecture and sustaining the activity of nitrogen metabolism enzymes—such as nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase (GOGAT)—in root and leaf tissues. Transcriptomic analysis indicated that V03 exhibits a broader transcriptional response (with more N Starvation-induced DEGs) and functional reprogramming in root tissues, showing stronger enrichment in stress-responsive processes, regulatory functions, and plasma membrane-related terms as well as environmental information processing pathways. Furthermore, V03 displayed more pronounced changes in the expression of genes related to N transport, N assimilation and transcription factor (TF) compared to the N starvation-sensitive variety V46. This study provides a robust and comprehensive methodology for evaluating N deficiency tolerance in semi-wild soybean. Our findings offer new insights into the physiological adaptions and molecular regulatory network governing N uptake and metabolism, which may support future breeding efforts aimed at enhancing NUE in leguminous crops.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111120"},"PeriodicalIF":5.7,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146158200","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}
Pub Date : 2026-02-05DOI: 10.1016/j.plaphy.2026.111121
Jingli Ding , Chenchen Ji , Wencong Han , Ao Zhang , Sheliang Wang , Chuang Wang , Guangda Ding , Lei Shi , Fangsen Xu , Hongmei Cai
Root system plays a crucial role in plant survival and normal growth. Identifying molecular determinants that optimize root system is an important strategy to improve yield production in crops. Here, we demonstrated an LRR-RLK (Leucine-Rich Repeat Receptor-Like Kinase), OsXIAO, which has an important function in rice root growth. The high expression level of OsXIAO was observed in rice roots, which was increased by IAA. Mutation of OsXIAO caused partially agravitropic root growth phenotype with short and curled roots, and severely repressed plant growth and grain production, while overexpressing of OsXIAO significantly promoted root growth and grain production. OsXIAO mutant showed reduced sensitivity to IAA and significantly lower IAA level in the root tips, while the overexpressing lines showed higher IAA level in the root tips. RNAseq analysis showed that 37 genes involved in auxin biosynthesis, signal transduction, and transmembrane transport were differentially expressed, and phosphoproteomic analyses revealed that the phosphorylation levels of 284th Thr and 288th Ser residues of OsPIN1a were significantly down-regulated in the roots of mutant. Moreover, Y2H (Yeast Two-Hybrid, LUC (Luciferase), and BIFC (Bimolecular Fluorescence Complementation) assays confirmed that OsXIAO could interact with OsPIN1a on the plasma membrane. Similar to OsXIAO, OsPIN1a was highly expressed in rice roots and induced by IAA, and the root growth was significantly inhibited in OsPIN1a mutants. Taken together, OsXIAO interacts with OsPIN1a on the plasma membrane and promoted auxin transport in rice roots, which improves root growth and elevates yield production.
{"title":"The LRR receptor-like kinase OsXIAO regulates rice root growth by interacting with auxin transporter OsPIN1a","authors":"Jingli Ding , Chenchen Ji , Wencong Han , Ao Zhang , Sheliang Wang , Chuang Wang , Guangda Ding , Lei Shi , Fangsen Xu , Hongmei Cai","doi":"10.1016/j.plaphy.2026.111121","DOIUrl":"10.1016/j.plaphy.2026.111121","url":null,"abstract":"<div><div>Root system plays a crucial role in plant survival and normal growth. Identifying molecular determinants that optimize root system is an important strategy to improve yield production in crops. Here, we demonstrated an LRR-RLK (Leucine-Rich Repeat Receptor-Like Kinase), OsXIAO, which has an important function in rice root growth. The high expression level of <em>OsXIAO</em> was observed in rice roots, which was increased by IAA. Mutation of <em>OsXIAO</em> caused partially agravitropic root growth phenotype with short and curled roots, and severely repressed plant growth and grain production, while overexpressing of <em>OsXIAO</em> significantly promoted root growth and grain production. <em>OsXIAO</em> mutant showed reduced sensitivity to IAA and significantly lower IAA level in the root tips, while the overexpressing lines showed higher IAA level in the root tips. RNAseq analysis showed that 37 genes involved in auxin biosynthesis, signal transduction, and transmembrane transport were differentially expressed, and phosphoproteomic analyses revealed that the phosphorylation levels of 284th Thr and 288th Ser residues of OsPIN1a were significantly down-regulated in the roots of mutant. Moreover, Y2H (Yeast Two-Hybrid, LUC (Luciferase), and BIFC (Bimolecular Fluorescence Complementation) assays confirmed that OsXIAO could interact with OsPIN1a on the plasma membrane. Similar to <em>OsXIAO</em>, <em>OsPIN1a</em> was highly expressed in rice roots and induced by IAA, and the root growth was significantly inhibited in <em>OsPIN1a</em> mutants. Taken together, OsXIAO interacts with OsPIN1a on the plasma membrane and promoted auxin transport in rice roots, which improves root growth and elevates yield production.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111121"},"PeriodicalIF":5.7,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146165319","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}
Pub Date : 2026-02-05DOI: 10.1016/j.plaphy.2026.111079
Wei Duan (段伟) , Qian Li (李倩) , Chun Liu (刘纯) , Xueli Zhang (张雪莉) , Lijun Liu (刘丽君) , Yaling Liu (刘亚玲) , Yongli Ran (冉永丽) , Yuxiang Wang (王玉祥) , Wanjun Zhang (张万军)
Medicago sativa (alfalfa), a vital perennial leguminous forage with economic and nutritional significance, is severely limited by drought stress. AP2/ERF transcription factors act as core modulators of plant responses to abiotic stresses. To improve alfalfa drought resistance, the MfERF053 gene cloned from Medicago falcata was introduced into the alfalfa genome. Its function and regulatory mechanism in alfalfa drought adaptation were investigated. We hypothesized that MfERF053 plays a pivotal role in drought resistance. Transgenic alfalfa lines overexpressing MfERF053 (OE) and ERF053 RNA interference (RNAi)-mediated alfalfa lines were developed. Drought resistance of OE, RNAi, and wild-type (WT) plants was assessed, alongside physiological phenotyping and RNA-seq profiling. The findings demonstrated that MfERF053 boosted alfalfa drought resistance. Specifically, OE lines exhibited a higher survival rate (68.05% vs. 12.96% in RNAi lines) and stronger water retention (29.45% leaf relative water content vs. 7.87% in RNAi lines). Their catalase and ascorbate peroxidase activities were also elevated, reactive oxygen species (ROS) accumulation was reduced, and photosynthetic function was stabilized (mitigated chlorophyll degradation and maintained PSII efficiency). RNA-seq analysis indicated that differentially expressed genes (DEGs) in OE plants were concentrated in three key pathways: abscisic acid (ABA) signaling, antioxidant defense, and photosynthetic pathways. Additionally, these DEGs synergistically regulate key genes within these pathways. This study verified the function of MfERF053 in drought resistance through multiple regulatory pathways. Furthermore, it provides novel insights into ERF-mediated drought resistance in alfalfa and offers a valuable molecular candidate for breeding drought-tolerant alfalfa varieties.
{"title":"Heterologous expression of MfERF053 enhances alfalfa drought resistance by regulating ABA signaling, antioxidant defense, and photosynthetic protection","authors":"Wei Duan (段伟) , Qian Li (李倩) , Chun Liu (刘纯) , Xueli Zhang (张雪莉) , Lijun Liu (刘丽君) , Yaling Liu (刘亚玲) , Yongli Ran (冉永丽) , Yuxiang Wang (王玉祥) , Wanjun Zhang (张万军)","doi":"10.1016/j.plaphy.2026.111079","DOIUrl":"10.1016/j.plaphy.2026.111079","url":null,"abstract":"<div><div><em>Medicago sativa</em> (alfalfa), a vital perennial leguminous forage with economic and nutritional significance, is severely limited by drought stress. AP2/ERF transcription factors act as core modulators of plant responses to abiotic stresses. To improve alfalfa drought resistance, the <em>MfERF053</em> gene cloned from <em>Medicago falcata</em> was introduced into the alfalfa genome. Its function and regulatory mechanism in alfalfa drought adaptation were investigated. We hypothesized that <em>MfERF053</em> plays a pivotal role in drought resistance. Transgenic alfalfa lines overexpressing <em>MfERF053</em> (OE) and <em>ERF053</em> RNA interference (RNAi)-mediated alfalfa lines were developed. Drought resistance of OE, RNAi, and wild-type (WT) plants was assessed, alongside physiological phenotyping and RNA-seq profiling. The findings demonstrated that <em>MfERF053</em> boosted alfalfa drought resistance. Specifically, OE lines exhibited a higher survival rate (68.05% vs. 12.96% in RNAi lines) and stronger water retention (29.45% leaf relative water content vs. 7.87% in RNAi lines). Their catalase and ascorbate peroxidase activities were also elevated, reactive oxygen species (ROS) accumulation was reduced, and photosynthetic function was stabilized (mitigated chlorophyll degradation and maintained PSII efficiency). RNA-seq analysis indicated that differentially expressed genes (DEGs) in OE plants were concentrated in three key pathways: abscisic acid (ABA) signaling, antioxidant defense, and photosynthetic pathways. Additionally, these DEGs synergistically regulate key genes within these pathways. This study verified the function of <em>MfERF053</em> in drought resistance through multiple regulatory pathways. Furthermore, it provides novel insights into ERF-mediated drought resistance in alfalfa and offers a valuable molecular candidate for breeding drought-tolerant alfalfa varieties.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111079"},"PeriodicalIF":5.7,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146143312","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}
Pub Date : 2026-02-05DOI: 10.1016/j.plaphy.2026.111119
Zhe Zhang , Yunfei Mao , Siying Huang , Yanni Li , Menglong Wu , Wenquan Niu , Runya Yang , Zhenhua Zhang
Aerated irrigation alleviates the high soil saturation issue caused by conventional irrigation by delivering oxygen-enriched water to the crop root zone. However, whether it can alleviate plant hypoxia under waterlogging stress remains unclear. In this study, we examined the effects of aeration on the growth, photosynthetic physiological activities, and gene expression of lettuce (Lactuca sativa L.) under different waterlogging durations (0, 4, and 8 days). The results indicate that under short-term waterlogging stress (≤4d), plants reduce the accumulation of reactive oxygen species by increasing the activity of the antioxidant system, and aeration does not significantly enhance plant growth. If waterlogging lasts for more than 8 days, non-aerated treatment leads to significant accumulation of reactive oxygen species (O2− and H2O2 increased by 50.68% and 37.76%, respectively), cell membrane damage (MDA increased by 32.31%), and damage to the photosynthetic system. At this point, aerated irrigation can significantly alleviate stress by increasing the expression of Psb and rbcS genes in leaves, maintaining normal photosynthetic function of lettuce, and increasing lettuce biomass by 36.70% compared to non-aerated treatment. Therefore, in actual waterlogging event management, aeration irrigation should be prioritized for long-term waterlogging (8d) areas. Twelve gene co-expression modules were identified using the weighted gene co-expression network analysis (WGCNA) method. Three modules specifically related to lettuce waterlogging stress were identified through correlation analysis with physiological indicators. The five hub genes (HPR3, GGPS1, THI1, rbcS, G6PD) in the yellow module have become sensitive genes that lead to a decrease in photosynthetic efficiency under waterlogging stress. The hub genes of brown and green modules (PPC4, FRO7, ispH, ERF1b, AUF2) showed an increase in expression levels with the passage of waterlogging time. These five genes may be the core genes for improving lettuce waterlogging tolerance. This study explored the molecular mechanism of lettuce's tolerance to waterlogging stress at the transcriptome level, providing deeper insights into the alleviating effect of aerated irrigation on waterlogging stress.
{"title":"Root-zone oxygen supply improves lettuce photosynthetic function under waterlogging stress and promotes plant growth","authors":"Zhe Zhang , Yunfei Mao , Siying Huang , Yanni Li , Menglong Wu , Wenquan Niu , Runya Yang , Zhenhua Zhang","doi":"10.1016/j.plaphy.2026.111119","DOIUrl":"10.1016/j.plaphy.2026.111119","url":null,"abstract":"<div><div>Aerated irrigation alleviates the high soil saturation issue caused by conventional irrigation by delivering oxygen-enriched water to the crop root zone. However, whether it can alleviate plant hypoxia under waterlogging stress remains unclear. In this study, we examined the effects of aeration on the growth, photosynthetic physiological activities, and gene expression of lettuce (<em>Lactuca sativa</em> L.) under different waterlogging durations (0, 4, and 8 days). The results indicate that under short-term waterlogging stress (≤4d), plants reduce the accumulation of reactive oxygen species by increasing the activity of the antioxidant system, and aeration does not significantly enhance plant growth. If waterlogging lasts for more than 8 days, non-aerated treatment leads to significant accumulation of reactive oxygen species (O<sub>2</sub><sup>−</sup> and H<sub>2</sub>O<sub>2</sub> increased by 50.68% and 37.76%, respectively), cell membrane damage (MDA increased by 32.31%), and damage to the photosynthetic system. At this point, aerated irrigation can significantly alleviate stress by increasing the expression of <em>Psb</em> and <em>rbcS</em> genes in leaves, maintaining normal photosynthetic function of lettuce, and increasing lettuce biomass by 36.70% compared to non-aerated treatment. Therefore, in actual waterlogging event management, aeration irrigation should be prioritized for long-term waterlogging (8d) areas. Twelve gene co-expression modules were identified using the weighted gene co-expression network analysis (WGCNA) method. Three modules specifically related to lettuce waterlogging stress were identified through correlation analysis with physiological indicators. The five hub genes (<em>HPR3</em>, <em>GGPS1</em>, <em>THI1</em>, <em>rbcS</em>, <em>G6PD</em>) in the yellow module have become sensitive genes that lead to a decrease in photosynthetic efficiency under waterlogging stress. The hub genes of brown and green modules (<em>PPC4</em>, <em>FRO7</em>, <em>ispH</em>, <em>ERF1b</em>, <em>AUF2</em>) showed an increase in expression levels with the passage of waterlogging time. These five genes may be the core genes for improving lettuce waterlogging tolerance. This study explored the molecular mechanism of lettuce's tolerance to waterlogging stress at the transcriptome level, providing deeper insights into the alleviating effect of aerated irrigation on waterlogging stress.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111119"},"PeriodicalIF":5.7,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146150469","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}
Pub Date : 2026-02-04DOI: 10.1016/j.plaphy.2026.111112
Peng Yang , Yuxin Qi , Yutong Cao , Xinlan Wang , Jiaxin Tan , Mingli Zhang , Yue Han , Xueshuang Huang
Benzylisoquinoline alkaloids (BIAs) are a notable class of bioactive natural products with therapeutic potential. Metabolomic profiling identified a total of 186 BIAs across various tissues of Eomecon chionantha, with sanguinarine and chelerythrine being the predominant compounds, quantified at 5.2 mg/g and 9.9 mg/g in the roots, respectively. The biosynthetic pathways for these compounds have been elucidated in species of the Papaveraceae family, where methylation events are crucial. Here, we present a telomere-to-telomere (T2T) gap-free genome assembly of E. chionantha, which has a total size of 368.5 Mb, comprising nine centromeric regions, 15 telomeres, 19,785 protein-coding genes, and 58.89% repetitive sequences. Genome analysis reveals a single whole-genome duplication in E. chionantha predating its divergence from Macleaya cordata (∼37.9 million years ago). Gene family analysis revealed the presence of 28 O-methyltransferase (OMT) genes in the E. chionantha genome, predominantly amplified through tandem duplication events, as well as the screening of EcOMT3/4/5/10/17/25/26/27 may be involved in the biosynthesis of sanguinarine and chelerythrine. Functional characterization demonstrated that all eight EcOMTs exhibit activity as 6OMT and scoulerine-9-O-methyltransferase (SMT), with only EcOMT17 functioning specifically as a 4′OMT, indicating that multiple EcOMTs have the catalytic capacity for 6OMT and SMT functions, while 4′OMT activity is highly specific. Collectively, this work elucidates OMT roles in BIA biosynthesis while offering genomic resources for Papaveraceae research and evolutionary insights into alkaloid diversification.
苄基异喹啉生物碱（BIAs）是一类具有显著生物活性的天然产物，具有治疗潜力。代谢组学分析共鉴定出186种BIAs，其中血根碱和车腥草碱是主要化合物，分别在根中含量为5.2 mg/g和9.9 mg/g。这些化合物的生物合成途径已经在木瓜科的物种中被阐明，其中甲基化事件是至关重要的。在这里，我们提出了一个端粒到端粒（T2T）无间隙的chionantha基因组组装，其总大小为368.5 Mb，包括9个着丝粒区，15个端粒，19,785个蛋白质编码基因和58.89%的重复序列。基因组分析显示，chionantha在其与Macleaya cordata（约3790万年前）分化之前就存在单个全基因组重复。基因家族分析显示，chionantha基因组中存在28个o -甲基转移酶（OMT）基因，主要通过串联重复事件扩增，以及EcOMT3/4/5/10/17/25/26/27可能参与血根碱和车麻碱的生物合成。功能表征表明，所有8个EcOMTs都具有6OMT和scoulerine-9- o -甲基转移酶（SMT）的活性，只有EcOMT17具有特异性的4'OMT功能，这表明多个EcOMTs具有6OMT和SMT功能的催化能力，而4'OMT活性具有高度特异性。总的来说，这项工作阐明了OMT在BIA生物合成中的作用，同时为罂粟科研究和生物碱多样化的进化见解提供了基因组资源。
{"title":"The gap-free genome and functional characterization of O-methyltransferases provide insights into the biosynthesis of sanguinarine and chelerythrine in Eomecon chionantha","authors":"Peng Yang , Yuxin Qi , Yutong Cao , Xinlan Wang , Jiaxin Tan , Mingli Zhang , Yue Han , Xueshuang Huang","doi":"10.1016/j.plaphy.2026.111112","DOIUrl":"10.1016/j.plaphy.2026.111112","url":null,"abstract":"<div><div>Benzylisoquinoline alkaloids (BIAs) are a notable class of bioactive natural products with therapeutic potential. Metabolomic profiling identified a total of 186 BIAs across various tissues of <em>Eomecon chionantha</em>, with sanguinarine and chelerythrine being the predominant compounds, quantified at 5.2 mg/g and 9.9 mg/g in the roots, respectively. The biosynthetic pathways for these compounds have been elucidated in species of the Papaveraceae family, where methylation events are crucial. Here, we present a telomere-to-telomere (T2T) gap-free genome assembly of <em>E. chionantha</em>, which has a total size of 368.5 Mb, comprising nine centromeric regions, 15 telomeres, 19,785 protein-coding genes, and 58.89% repetitive sequences. Genome analysis reveals a single whole-genome duplication in <em>E. chionantha</em> predating its divergence from <em>Macleaya cordata</em> (∼37.9 million years ago). Gene family analysis revealed the presence of 28 <em>O</em>-methyltransferase (<em>OMT</em>) genes in the <em>E. chionantha</em> genome, predominantly amplified through tandem duplication events, as well as the screening of EcOMT3/4/5/10/17/25/26/27 may be involved in the biosynthesis of sanguinarine and chelerythrine. Functional characterization demonstrated that all eight EcOMTs exhibit activity as 6OMT and scoulerine-9-<em>O</em>-methyltransferase (SMT), with only EcOMT17 functioning specifically as a 4′OMT, indicating that multiple EcOMTs have the catalytic capacity for 6OMT and SMT functions, while 4′OMT activity is highly specific. Collectively, this work elucidates OMT roles in BIA biosynthesis while offering genomic resources for Papaveraceae research and evolutionary insights into alkaloid diversification.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111112"},"PeriodicalIF":5.7,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142398","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}
Lignin deposition in plant cell walls influences plant growth and its production efficiency in industry. The lignification process involves complex biosynthetic pathways requiring coordinated gene interactions and is regulated by transcriptional networks mediated through transcription factor-DNA interactions. In Salix matsudana, exogenous ethephon application induced a dwarfing phenotype with reduced lignin accumulation in stems. Transcriptomic analysis of ethephon-treated samples identified Sm4CL11, a key gene involved in lignin biosynthesis. Virus-induced gene silencing (VIGS) of Sm4CL11 reproduced the dwarfing phenotype and decreased lignin deposition. Histochemical staining and Raman microspectroscopy revealed that Sm4CL11 regulates lignin content and spatial deposition patterns in vessel cell walls, confirming its essential role in the lignin biosynthetic pathway. WGCNA and promoter cis-element analysis identified SmERF B3-4, an upstream transcriptional regulator of Sm4CL11. Yeast one-hybrid assays and dual luciferase reporter assay (LUC) assays demonstrated direct binding of SmERF B3-4 to the Sm4CL11 promoter, activating its expression. This study elucidates molecular mechanisms underlying lignin biosynthesis regulation and provides valuable insights for which would contribute to the lignin-related chemical industry.
{"title":"Molecular mechanism of SmERF B3-4 in regulating lignin biosynthesis by modulating Sm4CL11 in Salix matsudana","authors":"Yiting Wang , Yanhong Chen , Tingting Chen , Jinglan Ni , Leting Wu , Hanrui Hao , Chunmei Yu , Fei Zhong , Hui Wei , Jian Zhang , Guoyuan Liu","doi":"10.1016/j.plaphy.2026.111106","DOIUrl":"10.1016/j.plaphy.2026.111106","url":null,"abstract":"<div><div>Lignin deposition in plant cell walls influences plant growth and its production efficiency in industry. The lignification process involves complex biosynthetic pathways requiring coordinated gene interactions and is regulated by transcriptional networks mediated through transcription factor-DNA interactions. In <em>Salix matsudana</em>, exogenous ethephon application induced a dwarfing phenotype with reduced lignin accumulation in stems. Transcriptomic analysis of ethephon-treated samples identified <em>Sm4CL11</em>, a key gene involved in lignin biosynthesis. Virus-induced gene silencing (VIGS) of <em>Sm4CL11</em> reproduced the dwarfing phenotype and decreased lignin deposition. Histochemical staining and Raman microspectroscopy revealed that <em>Sm4CL11</em> regulates lignin content and spatial deposition patterns in vessel cell walls, confirming its essential role in the lignin biosynthetic pathway. WGCNA and promoter cis-element analysis identified <em>SmERF B3-4</em>, an upstream transcriptional regulator of <em>Sm4CL11</em>. Yeast one-hybrid assays and dual luciferase reporter assay (LUC) assays demonstrated direct binding of <em>SmERF B3-4</em> to the <em>Sm4CL11</em> promoter, activating its expression. This study elucidates molecular mechanisms underlying lignin biosynthesis regulation and provides valuable insights for which would contribute to the lignin-related chemical industry.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111106"},"PeriodicalIF":5.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122709","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}
Pub Date : 2026-02-03DOI: 10.1016/j.plaphy.2026.111054
Jianbin Li , Rurou Long , Michael Ackah , Frank Kwarteng Amoako , Andrews Danquah , Meina Zhu , Hanfa Shahid , Carlos Kwesi Tettey , Owuraku Amponsah Abu , Xueying Jin , Mengdi Zhao , Weiguo Zhao
Plants have evolved intricate and sophisticated mechanisms to sense and respond to boron (B) stresses. Alterations to the cell wall and other molecular pathways are strategies that help plants adapt to B stresses by cross-linking with rhamnogalacturonan II (RG-II) to form borate-dimers. However, the molecular mechanism by which cell wall components and organization respond to B stresses is not fully understood in mulberry plants. This study, via conjoint transcriptomics-metabolomics and virus-induced gene silencing analyses, aimed to explore the diverse B stress response mechanisms and functionally characterize the role of MaXTH23 in cell wall remodeling in mulberry leaves subjected to different levels of B, ranging from deficiency (0 mM; T1), sufficiency (0.1 mM; control, CK), moderate deficiency (0.02 mM; T2), toxicity (0.5 and 1.0 mM as T3 and T4, respectively) and cultivated under greenhouse conditions. The analyses identified a total of 6114 and 441 differentially expressed genes (DEGs) and metabolites (DEMs), respectively, in the different KEGG pathways in the separate omics analysis for all treatments. However, our conjoint analysis identified 1120 DEGs associated with 78 DEMs and were significantly co-enriched in 96 different KEGG pathways. Meanwhile, the functional characterization via silencing of MaXTH23 did not nullify its function in cell wall modification and remodeling but concomitantly caused significant increases in total pectin and water-soluble pectin contents, quintessentially promoting pectin cross-linking in the cell wall. This study highlights a novel perspective for identifying and characterizing the regulatory functions of MaXTH23 and the B-induced pathways and tolerance mechanisms employed by mulberry plants.
{"title":"Integrated transcriptomic and metabolomic profiling and functional characterization of the MaXTH23 gene in boron stress adaptation in mulberry (Morus alba L.)","authors":"Jianbin Li , Rurou Long , Michael Ackah , Frank Kwarteng Amoako , Andrews Danquah , Meina Zhu , Hanfa Shahid , Carlos Kwesi Tettey , Owuraku Amponsah Abu , Xueying Jin , Mengdi Zhao , Weiguo Zhao","doi":"10.1016/j.plaphy.2026.111054","DOIUrl":"10.1016/j.plaphy.2026.111054","url":null,"abstract":"<div><div>Plants have evolved intricate and sophisticated mechanisms to sense and respond to boron (B) stresses. Alterations to the cell wall and other molecular pathways are strategies that help plants adapt to B stresses by cross-linking with rhamnogalacturonan II (RG-II) to form borate-dimers. However, the molecular mechanism by which cell wall components and organization respond to B stresses is not fully understood in mulberry plants. This study, via conjoint transcriptomics-metabolomics and virus-induced gene silencing analyses, aimed to explore the diverse B stress response mechanisms and functionally characterize the role of <em>MaXTH23</em> in cell wall remodeling in mulberry leaves subjected to different levels of B, ranging from deficiency (0 mM; T1), sufficiency (0.1 mM; control, CK), moderate deficiency (0.02 mM; T2), toxicity (0.5 and 1.0 mM as T3 and T4, respectively) and cultivated under greenhouse conditions. The analyses identified a total of 6114 and 441 differentially expressed genes (DEGs) and metabolites (DEMs), respectively, in the different KEGG pathways in the separate omics analysis for all treatments. However, our conjoint analysis identified 1120 DEGs associated with 78 DEMs and were significantly co-enriched in 96 different KEGG pathways. Meanwhile, the functional characterization via silencing of <em>MaXTH23</em> did not nullify its function in cell wall modification and remodeling but concomitantly caused significant increases in total pectin and water-soluble pectin contents, quintessentially promoting pectin cross-linking in the cell wall. This study highlights a novel perspective for identifying and characterizing the regulatory functions of <em>MaXTH23</em> and the B-induced pathways and tolerance mechanisms employed by mulberry plants.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111054"},"PeriodicalIF":5.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122652","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}
Pub Date : 2026-02-03DOI: 10.1016/j.plaphy.2026.111105
Wenhui Lv , Manqiao Li , Yueyue Zhu , Kuixiu Li , Zihan Yang , Junliang Li , Fugang Wei , Shengchao Yang , Xuyan Liu , Guanze Liu
Panax notoginseng is highly susceptible to root rot during cultivation, severely affecting its production and quality. Phospholipases participate in plant immunity by producing free fatty acids and conjugated lipids that activate downstream signaling cascades. However, genome-wide identification of PnPL genes in P. notoginseng remains limited. A total of 72 PnPL genes were identified in P. notoginseng: 48 PnPLA genes, 9 PnPLC genes and 15 PnPLD genes. Transcriptome and qRT-PCR analyses between healthy and diseased plants (CK, RⅠ and RⅡ) revealed 13 differentially expressed genes from PnPL Gene Family, 11 of which belonged to the PnPLA genes superfamily. Notably, PnPLA1-8 exhibited sustained upregulation with worsening root rot. Further, RNA interference (RNAi) mediated silencing of PnPLA1-8 gene increased susceptibility to Fusarium oxysporum that the main pathogenic fungus in P. notoginseng, whereas overexpression of PnPLA1-8 gene in Nicotiana tabacum enhanced resistance to F. oxysporum. This study suggests that the PnPLA1-8 genes exhibit potential roles in resistance to F. oxysporum.
{"title":"Genome-wide identification of the phospholipase gene family in Panax notoginseng and functional analysis of PnPLA1-8 response to Fusarium oxysporum infection","authors":"Wenhui Lv , Manqiao Li , Yueyue Zhu , Kuixiu Li , Zihan Yang , Junliang Li , Fugang Wei , Shengchao Yang , Xuyan Liu , Guanze Liu","doi":"10.1016/j.plaphy.2026.111105","DOIUrl":"10.1016/j.plaphy.2026.111105","url":null,"abstract":"<div><div><em>Panax notoginseng</em> is highly susceptible to root rot during cultivation, severely affecting its production and quality. Phospholipases participate in plant immunity by producing free fatty acids and conjugated lipids that activate downstream signaling cascades. However, genome-wide identification of PnPL genes in <em>P. notoginseng</em> remains limited. A total of 72 PnPL genes were identified in <em>P. notoginseng</em>: 48 PnPLA genes, 9 PnPLC genes and 15 PnPLD genes. Transcriptome and qRT-PCR analyses between healthy and diseased plants (CK, RⅠ and RⅡ) revealed 13 differentially expressed genes from PnPL Gene Family, 11 of which belonged to the PnPLA genes superfamily. Notably, <em>PnPLA1-8</em> exhibited sustained upregulation with worsening root rot. Further, RNA interference (RNAi) mediated silencing of <em>PnPLA1-8</em> gene increased susceptibility to <em>Fusarium oxysporum</em> that the main pathogenic fungus in <em>P. notoginseng</em>, whereas overexpression of <em>PnPLA1-8</em> gene in <em>Nicotiana tabacum</em> enhanced resistance to <em>F. oxysporum</em>. This study suggests that the <em>PnPLA1-8</em> genes exhibit potential roles in resistance to <em>F. oxysporum</em>.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111105"},"PeriodicalIF":5.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146143355","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}
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