Molecular Plant最新文献

{"title":"GEFormer: A genotype-environment interaction-based genomic prediction method that integrates the gating multilayer perceptron and linear attention mechanisms.","authors":"Zhou Yao, Mengting Yao, Chuang Wang, Ke Li, Junhao Guo, Yingjie Xiao, Jianbing Yan, Jianxiao Liu","doi":"10.1016/j.molp.2025.01.020","DOIUrl":"10.1016/j.molp.2025.01.020","url":null,"abstract":"<p><p>The integration of genotypic and environmental data can enhance genomic prediction accuracy for crop field traits. Existing genomic prediction methods fail to consider environmental factors and the real growth environments of crops, resulting in low genomic prediction accuracy. In this work, we developed GEFormer, a genotype-environment interaction genomic prediction method that integrates gating multilayer perceptron (gMLP) and linear attention mechanisms. First, GEFormer uses gMLP to extract local and global features among SNPs. Then, Omni-dimensional Dynamic Convolution is used to extract the dynamic and comprehensive features of multiple environmental factors within each day, taking into consideration the real growth pattern of crops. A linear attention mechanism is used to capture the temporal features of environmental changes. Finally, GEFormer uses a gating mechanism to effectively fuse the genomic and environmental features. We examined the accuracy of GEFormer for predicting important agronomic traits of maize, rice, and wheat under three experimental scenarios: untested genotypes in tested environments, tested genotypes in untested environments, and untested genotypes in untested environments. The results showed that GEFormer outperforms six cutting-edge statistical learning methods and four machine learning methods, especially with great advantages under the scenario of untested genotypes in untested environments. In addition, we used GEFormer for three real-world breeding applications: phenotype prediction in unknown environments, hybrid phenotype prediction using an inbred population, and cross-population phenotype prediction. The results showed that GEFormer had better prediction performance in actual breeding scenarios and could be used to assist in crop breeding.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"527-549"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066845","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":"Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid.","authors":"Kai Jiang, Birger Lindberg Møller, Shaofan Luo, Yu Yang, David R Nelson, Elizabeth Heather Jakobsen Neilson, Joachim Møller Christensen, Kai Hua, Chao Hu, Xinhua Zeng, Mohammed Saddik Motawie, Tao Wan, Guang-Wan Hu, Guy Eric Onjalalaina, Yijiao Wang, Juan Diego Gaitán-Espitia, Zhiwen Wang, Xiao-Yan Xu, Jiamin He, Linying Wang, Yuanyuan Li, Dong-Hui Peng, Siren Lan, Huiming Zhang, Qing-Feng Wang, Zhong-Jian Liu, Wei-Chang Huang","doi":"10.1016/j.molp.2024.12.010","DOIUrl":"10.1016/j.molp.2024.12.010","url":null,"abstract":"<p><p>Angraecum sesquipedale, also known as Darwin's orchid, possesses an exceptionally long nectar spur. Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis, later identified as Xanthopan praedicta. In this plant-pollinator interaction, the A. sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes (R₁R₂C = N-OH) to attract crepuscular and nocturnal pollinators. The molecular mechanism of oxime biosynthesis remains unclear in orchids. Here, we present the chromosome-level genome of A. sesquipedale. The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes. Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A. sesquipedale genome nor the genomes of other members of the orchid family. Metabolomic analysis of the A. sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage. By integrating metabolomic and transcriptomic correlation approaches, flavin-containing monooxygenases (FMOs) encoded by six tandem-repeat genes in the A. sesquipedale genome are identified as catalyzing the formation of oximes present. Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis. We designate these FMOs as orchid oxime synthases 1-6. The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin's orchid provide new insights into the convergent evolution of biosynthetic pathways.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"392-415"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864900","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":"Chloroplast state transitions modulate nuclear genome stability via cytokinin signaling in Arabidopsis.","authors":"Yajun Zeng, Sujuan Duan, Yawen Wang, Zhifeng Zheng, Zeyi Wu, Meihui Shi, Manchun Wang, Lan Jiang, Xue Li, Hong-Bin Wang, Hong-Lei Jin","doi":"10.1016/j.molp.2025.01.021","DOIUrl":"10.1016/j.molp.2025.01.021","url":null,"abstract":"<p><p>Activities of the chloroplasts and nucleus are coordinated by retrograde signaling, which play crucial roles in plant development and environmental adaptation. However, the connection between chloroplast status and nuclear genome stability is poorly understood. Chloroplast state transitions enable the plant to balance photosystem absorption capacity in an environment with changing light quality. Here, we report that abnormal chloroplast state transitions lead to instability in the nuclear genome and impaired plant growth. We observed increased DNA damage in the state transition-defective Arabidopsis thaliana mutant stn7, and demonstrated that this damage was triggered by cytokinin accumulation and activation of cytokinin signaling. We showed that cytokinin signaling promotes a competitive association between ARABIDOPSIS RESPONSE REGULATOR 10 (ARR10) with PROLIFERATING CELLULAR NUCLEAR ANTIGEN 1/2 (PCNA1/2), inhibiting the binding of PCNA1/2 to nuclear DNA. This affects DNA replication, leading to replication-dependent genome instability. Treatment with 2,5-dibromo-3-methyl-6-isopropylbenzoquinone that simulates the reduction of the plastoquinone pool during abnormal state transitions increased the accumulation of ARABIDOPSIS HISTIDINE-CONTAINING PHOSPHOTRANSMITTER 1, a phosphotransfer protein involved in cytokinin signaling, and promoted the interaction between ARR10 with PCNA1/2, leading to increased DNA damage. These findings highlight the function of cytokinin signaling in coordinating chloroplast function and nuclear genome integrity during plant acclimation to environmental changes.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"513-526"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066843","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":"New molecular chaperone roles for CO₂ assimilation in early land plants.","authors":"Julie L McDonald, Robert H Wilson","doi":"10.1016/j.molp.2025.01.015","DOIUrl":"10.1016/j.molp.2025.01.015","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"386-388"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008776","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":"Sculpting the growth-defense trade-off by H₂S.","authors":"Hongfei Li, Yanjie Xie","doi":"10.1016/j.molp.2025.01.023","DOIUrl":"10.1016/j.molp.2025.01.023","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"389-391"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066847","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":"A small RNA effector conserved in herbivore insects suppresses host plant defense by cross-kingdom gene silencing.","authors":"Wen-Hao Han, Shun-Xia Ji, Feng-Bin Zhang, Hong-Da Song, Jun-Xia Wang, Xiao-Ping Fan, Rui Xie, Shu-Sheng Liu, Xiao-Wei Wang","doi":"10.1016/j.molp.2025.01.001","DOIUrl":"10.1016/j.molp.2025.01.001","url":null,"abstract":"<p><p>Herbivore insects deploy salivary effectors to manipulate the defense of their host plants. However, it remains unclear whether small RNAs from insects can function as effectors in regulating plant-insect interactions. Here, we report that a microRNA (miR29-b) found in the saliva of the phloem-feeding whitefly (Bemisia tabaci) can transfer into the host plant phloem during feeding and fine-tune the defense response of tobacco (Nicotiana tabacum) plants. We show that the salivary gland-enriched BtmiR29-b is produced by BtDicer 1 and released into tobacco cells via salivary exosomes. Once inside the plant cells, BtmiR29-b hijacks tobacco Argonaute 1 to silence the defense gene Bcl-2-associated athanogene 4 (NtBAG4). In tobacco, NtBAG4 acts as the positive regulator of phytohormones salicylic acid (SA) and jasmonic acid (JA), enhancing plant defense against whitefly attacks. Interestingly, we also found that miR29-b acts as a salivary effector in another Hemipteran insect, the aphid Myzus persicae, which inhibits tobacco resistance by degrading NtBAG4. Moreover, miR29-b is highly conserved in Hemiptera and across other insect orders such as Coleoptera, Hymenoptera, Orthoptera, and Blattaria. Computational analysis suggests that miR29-b may also target the evolutionarily conserved BAG4 gene in other plant species. We further provide evidence showing BtmiR29-b-mediated BAG4 cleavage and defense suppression in tomato (Solanum lycopersicum). Taken together, our work reveals that a conserved miR29-b effector from insects fine-tunes plant SA- and JA-mediated defense by cross-kingdom silencing of the host plant BAG4 gene, providing new insight into the defense and counter-defense mechanisms between herbivores and their host plants.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"437-456"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927648","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":"A typical NLR recognizes a family of structurally conserved effectors to confer plant resistance against adapted and non-adapted Phytophthora pathogens.","authors":"Xiaohua Dong, Xu Lu, Hai Zhu, Zhengxue Zhu, Peiyun Ji, Xianglan Li, Tianli Li, Xiong Zhang, Gan Ai, Daolong Dou","doi":"10.1016/j.molp.2025.01.018","DOIUrl":"10.1016/j.molp.2025.01.018","url":null,"abstract":"<p><p>Plants possess remarkably durable resistance against non-adapted pathogens in nature. However, the underlying molecular mechanisms remain poorly understood, and it is unclear how the resistance is maintained without coevolution between hosts and non-adapted pathogens. In this study, we used Phytophthora sojae (Ps), a non-adapted pathogen of Nicotiana benthamiana (Nb), as a model and identified an RXLR effector that determines Nb incompatibility to Ps. Knockout of this RXLR effector in Ps enables successful infection of Nb, leading us to name it AvrNb (Avirulence gene in Nb). A systematic screening of Nb NLR genes further revealed that NbPrf, previously reported to be a receptor of bacterial avirulence proteins, is the NLR protein responsible for mediating AvrNb recognition and initiating the hypersensitive response (HR). Mutation in NbPrf makes Nb completely compatible to Ps. We found that AvrNb is structurally conserved among multiple Phytophthora pathogens, and its homologs also induce NbPrf-dependent HR. Remarkably, further inoculation assay showed that NbPrf is also involved in plant immunity to two adapted Phytophthora pathogens, Phytophthora infestans and Phytophthora capsici. Our findings suggest that NbPrf represents a promising resource for breeding resistance to Phytophthora pathogens and implicate that the conserved effectors present in both adapted and non-adapted pathogens may provide sufficient selective pressure to maintain the remarkably durable incompatibility between plants and non-adapted pathogens.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"485-500"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040158","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":"Getting the SCOOP on peptide ligands that regulate leaf senescence.","authors":"Judy A Brusslan","doi":"10.1016/j.molp.2025.01.013","DOIUrl":"10.1016/j.molp.2025.01.013","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"384-385"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008773","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":"NTRC mediates the coupling of chloroplast redox rhythm with nuclear circadian clock in plant cells.","authors":"Seol Ki Paeng, Seong Dong Wi, Ho Byoung Chae, Su Bin Bae, Kieu Anh Thi Phan, Min Gab Kim, Dae-Jin Yun, Woe-Yeon Kim, C Robertson McClung, Sang Yeol Lee","doi":"10.1016/j.molp.2025.01.014","DOIUrl":"10.1016/j.molp.2025.01.014","url":null,"abstract":"<p><p>The intricate interplay between cellular circadian rhythms, primarily manifested in the chloroplast redox oscillations-characterized by diel hyperoxidation/reduction cycles of 2-Cys peroxiredoxins-and the nuclear transcription/translation feedback loop (TTFL) machinery within plant cells, demonstrates a remarkable temporal coherence. However, the molecular mechanisms underlying the integration of these circadian rhythms remain elusive. In this study, we reveal that the chloroplast redox protein, NADPH-dependent thioredoxin reductase type C (NTRC), modulates the integration of the chloroplast redox rhythms and nuclear circadian clocks by regulating intracellular levels of reactive oxygen species and sucrose. In NTRC-deficient ntrc mutants, the perturbed temporal dynamics of cytosolic metabolite pools substantially attenuate the amplitude of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) mRNA oscillation while maintaining its inherent periodicity. In contrast, these fluctuations extend the period and greatly reduced the amplitude of GIGANTEA (GI). In alignment with its regulatory role, the chloroplast redox rhythm and TTFL-driven nuclear oscillators are severely disrupted in ntrc plants. The impairements are rescued by NTRC expression but not by the expression of catalytically inactive NTRC(C/S) mutant, indicating that NTRC's redox activity is essential for synchronizing intracellular circadian rhythms. In return, the canonical nuclear clock component, TIMING OF CAB EXPRESSION 1 (TOC1), regulates the diel chloroplast redox rhythm by controlling NTRC expression, as evidenced by the redox cycle of chloroplast 2-Cys peroxiredoxins. This reciprocal regulation suggests a tight coupling between chloroplast redox rhythms and nuclear oscillators. Collectively, our study has identified NTRC as a key circadian modulator, elucidating the intricate connection between the metabolite-dependent chloroplast redox rhythm and the temporal dynamics of nuclear canonical clocks.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"468-484"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008777","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":"TIR-mediated immune signaling through the EDS1:PAD4:ADR1 node is conserved in monocots and dicots.","authors":"Natsumi Maruta, Mitchell Sorbello, Bostjan Kobe","doi":"10.1016/j.molp.2024.12.017","DOIUrl":"https://doi.org/10.1016/j.molp.2024.12.017","url":null,"abstract":"<p><p>Plants defend themselves against pathogens by activating two interconnected layers of immunity: pattern- and effector-triggered immunity. Recent studies shed light on a number of unanswered questions in these pathways and demonstrate a conserved structural basis, in monocots and dicots, of signaling through the EDS1:PAD4:ADR1 module, downstream of Toll/interleukin-1 receptor (TIR) domain-containing immune receptors that cleave the dinucleotide nicotinamide adenine dinucleotide (NAD⁺). The studies define a new function for TIR domain proteins in monocots and suggest that the signaling molecule 5″-phosphoribosyl (pRib)-AMP is derived from the TIR product 2'-adenosine diphosphate ribose (2'cADPR). These findings have important implications for developing the strategies to breed resistant crops.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"18 2","pages":"192-194"},"PeriodicalIF":17.1,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151304","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}