As drought severely threatens the stability of crop yields, it is crucial to develop cultivars with enhanced drought resilience. Here we demonstrate that natural variation in ZmDapF1, encoding a putative diaminopimelate epimerase, contributes to maize drought-stress resistance without compromising grain yield. ZmDapF1 inhibits the activity of ZmMDH6, a chloroplast NADP-dependent malate dehydrogenase. ZmDapF1 gene knockout mutants exhibited significantly enhanced seedling viability and grain yield under drought stress, while maintaining high yields under normal field conditions. Natural variations in the ZmDapF1 promoter increase its binding affinity to a MYB transcription factor, ZmMYB121, which represses ZmDapF1 expression under drought. Therefore, ZmMYB121 plays a positive role in drought resistance. Knocking out ZmDapF1 resulted in increased ZmMDH6 activity, enhanced photosynthetic rate and reduced reactive oxygen species accumulation under drought, which may confer the enhanced drought resilience. Thus, genetic engineering targeting ZmDapF1 holds great potential for developing maize varieties with improved drought resilience. In maize, ZmDapF1 suppresses the activity of ZmMDH6 in chloroplasts, exacerbating oxidative damage under drought. Knocking out ZmDapF1 or using its favourable allele with lower gene expression enhances drought resilience without yield penalty.
{"title":"Natural variation in ZmDapF1 enhances maize drought resilience","authors":"Yongyan Lian, Shiping Yang, Tian Tian, Zhirui Yang, Shengxue Liu, Xiaomeng Fu, Chenyi Liu, Tengfei Zhu, Yijie Wang, Yunting Bai, Ziyang Wang, Chen Wang, Yunlu Shi, Yue Li, Yanjun Zhang, Xingrong Wang, Xiaohong Yang, Feng Qin","doi":"10.1038/s41477-025-02141-3","DOIUrl":"10.1038/s41477-025-02141-3","url":null,"abstract":"As drought severely threatens the stability of crop yields, it is crucial to develop cultivars with enhanced drought resilience. Here we demonstrate that natural variation in ZmDapF1, encoding a putative diaminopimelate epimerase, contributes to maize drought-stress resistance without compromising grain yield. ZmDapF1 inhibits the activity of ZmMDH6, a chloroplast NADP-dependent malate dehydrogenase. ZmDapF1 gene knockout mutants exhibited significantly enhanced seedling viability and grain yield under drought stress, while maintaining high yields under normal field conditions. Natural variations in the ZmDapF1 promoter increase its binding affinity to a MYB transcription factor, ZmMYB121, which represses ZmDapF1 expression under drought. Therefore, ZmMYB121 plays a positive role in drought resistance. Knocking out ZmDapF1 resulted in increased ZmMDH6 activity, enhanced photosynthetic rate and reduced reactive oxygen species accumulation under drought, which may confer the enhanced drought resilience. Thus, genetic engineering targeting ZmDapF1 holds great potential for developing maize varieties with improved drought resilience. In maize, ZmDapF1 suppresses the activity of ZmMDH6 in chloroplasts, exacerbating oxidative damage under drought. Knocking out ZmDapF1 or using its favourable allele with lower gene expression enhances drought resilience without yield penalty.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2381-2394"},"PeriodicalIF":13.6,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145396880","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}
Pub Date : 2025-10-29DOI: 10.1038/s41477-025-02142-2
Malia L. Moore, Nicholas Allsing, Nolan T. Hartwick, Allen Mamerto, Emily R. Murray, Rilee D. Sanders, Todd P. Michael
The temperate seagrass Zostera marina is a foundational marine species that provides critical habitat in bays and estuaries throughout the Northern Hemisphere. Human activities and climatic events have necessitated Z. marina restoration, for which high transplant mortality rates call for innovative cross-disciplinary solutions. We identify a hybrid between Z. marina and Z. pacifica and explore the hybrid population as a tool for restoration from a genomic perspective. Among several habitat distinctions, Z. pacifica, an endemic to the Southern California Bight (West Coast, USA), is deeper-living and may encode resilience to low light, a leading factor of seagrass restoration failure. We construct a haplotype-resolved chromosome-scale genome assembly of the hybrid and several California Zostera accessions to describe the divergence between Z. marina and Z. pacifica and characterize the hybrid’s stage of maturity as an F1. Transcriptomes of Z. marina and the hybrid subjected to reduced light in an experimental mesocosm reveal divergent trends in photosynthesis, carbohydrate utilization and stress responses. Photoperiod regulation by Z. pacifica orthologues of key circadian clock genes, prominently LATE ELONGATED HYPOCOTYL and WITH NO-LYSINE KINASEs, may drive this response. By describing the hybridization event using genomic and transcriptomic methods, this study presents preliminary evidence of low-light tolerance modulated by a labile circadian clock to motivate further ecological and functional studies of this hybrid as an experimental tool to access Z. pacifica genetics and its relevance to restoration. Seagrass genomes of the deep-water Zostera pacifica and shallow-water Z. marina from the Eastern Pacific Ocean provide evidence for low-light adaptation exemplified in the wild hybrid Z. marina × pacifica subjected to low-light stress in aquaria.
{"title":"Hybridization and low-light adaptability in California eelgrass (Zostera spp.)","authors":"Malia L. Moore, Nicholas Allsing, Nolan T. Hartwick, Allen Mamerto, Emily R. Murray, Rilee D. Sanders, Todd P. Michael","doi":"10.1038/s41477-025-02142-2","DOIUrl":"10.1038/s41477-025-02142-2","url":null,"abstract":"The temperate seagrass Zostera marina is a foundational marine species that provides critical habitat in bays and estuaries throughout the Northern Hemisphere. Human activities and climatic events have necessitated Z. marina restoration, for which high transplant mortality rates call for innovative cross-disciplinary solutions. We identify a hybrid between Z. marina and Z. pacifica and explore the hybrid population as a tool for restoration from a genomic perspective. Among several habitat distinctions, Z. pacifica, an endemic to the Southern California Bight (West Coast, USA), is deeper-living and may encode resilience to low light, a leading factor of seagrass restoration failure. We construct a haplotype-resolved chromosome-scale genome assembly of the hybrid and several California Zostera accessions to describe the divergence between Z. marina and Z. pacifica and characterize the hybrid’s stage of maturity as an F1. Transcriptomes of Z. marina and the hybrid subjected to reduced light in an experimental mesocosm reveal divergent trends in photosynthesis, carbohydrate utilization and stress responses. Photoperiod regulation by Z. pacifica orthologues of key circadian clock genes, prominently LATE ELONGATED HYPOCOTYL and WITH NO-LYSINE KINASEs, may drive this response. By describing the hybridization event using genomic and transcriptomic methods, this study presents preliminary evidence of low-light tolerance modulated by a labile circadian clock to motivate further ecological and functional studies of this hybrid as an experimental tool to access Z. pacifica genetics and its relevance to restoration. Seagrass genomes of the deep-water Zostera pacifica and shallow-water Z. marina from the Eastern Pacific Ocean provide evidence for low-light adaptation exemplified in the wild hybrid Z. marina × pacifica subjected to low-light stress in aquaria.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2409-2422"},"PeriodicalIF":13.6,"publicationDate":"2025-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02142-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145382469","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}
Pub Date : 2025-10-27DOI: 10.1038/s41477-025-02152-0
Richard Flavell, Jeff Rosichan, Jiemeng Xu, Matthew Reynolds
{"title":"Rethinking the need for field trials","authors":"Richard Flavell, Jeff Rosichan, Jiemeng Xu, Matthew Reynolds","doi":"10.1038/s41477-025-02152-0","DOIUrl":"10.1038/s41477-025-02152-0","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2185-2186"},"PeriodicalIF":13.6,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145373839","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}
Chromatin and transcription states are crucial for establishing and maintaining gene regulation and genome integrity, governed by a complex network of epigenetic modifications. Despite significant advancements, the interplay between epitranscriptomic and epigenetic modifications in transcriptional regulation and chromatin state remains elusive in plants. Here we profile a comprehensive spectrum of N6-methyladenosine (m6A) on chromatin-associated RNAs, especially retrotransposon transcripts, in Arabidopsis. We show that m6A writer subunits FIP37 and VIR mediate the methylation of retrotransposon RNAs, which are recognized by the nuclear m6A reader proteins CPSF30-L and ECT12, leading to a closed heterochromatin state and transcription suppression of m6A retrotransposon RNAs. Through monitoring nuclear RNA stability and transcription rate upon the depletion of either writer or reader, we provide evidence consistent with a model in which CPSF30-L associates with SUVH4/5/6 and ATXR5/6 and contributes to histone H3 K9 dimethylation and H3 K27 monomethylation at m6A-marked retrotransposons. Our findings elucidate a regulatory mechanism involving RNA m6A formation and recognition, coupled with histone modifications, thereby highlighting the intricate epitranscriptomic and epigenetic interplay in plant physiological and biological processes. This study reports that m6A on retrotransposon RNAs is recognized by nuclear readers CPSF30-L and ECT12, which associate with SUVH4/5/6 and ATXR5/6 to enhance H3 K9 dimethylation and H3 K27 monomethylation at specific sites, thereby leading to closed heterochromatin states and transcriptional silencing.
{"title":"RNA m6A regulates the transcription and heterochromatin state of retrotransposons in Arabidopsis","authors":"Peizhe Song, Zhihe Cai, Subiding Tayier, Enlin Tian, Zixin Chen, Kemiao Yu, Lixiang Liu, Guifang Jia","doi":"10.1038/s41477-025-02137-z","DOIUrl":"10.1038/s41477-025-02137-z","url":null,"abstract":"Chromatin and transcription states are crucial for establishing and maintaining gene regulation and genome integrity, governed by a complex network of epigenetic modifications. Despite significant advancements, the interplay between epitranscriptomic and epigenetic modifications in transcriptional regulation and chromatin state remains elusive in plants. Here we profile a comprehensive spectrum of N6-methyladenosine (m6A) on chromatin-associated RNAs, especially retrotransposon transcripts, in Arabidopsis. We show that m6A writer subunits FIP37 and VIR mediate the methylation of retrotransposon RNAs, which are recognized by the nuclear m6A reader proteins CPSF30-L and ECT12, leading to a closed heterochromatin state and transcription suppression of m6A retrotransposon RNAs. Through monitoring nuclear RNA stability and transcription rate upon the depletion of either writer or reader, we provide evidence consistent with a model in which CPSF30-L associates with SUVH4/5/6 and ATXR5/6 and contributes to histone H3 K9 dimethylation and H3 K27 monomethylation at m6A-marked retrotransposons. Our findings elucidate a regulatory mechanism involving RNA m6A formation and recognition, coupled with histone modifications, thereby highlighting the intricate epitranscriptomic and epigenetic interplay in plant physiological and biological processes. This study reports that m6A on retrotransposon RNAs is recognized by nuclear readers CPSF30-L and ECT12, which associate with SUVH4/5/6 and ATXR5/6 to enhance H3 K9 dimethylation and H3 K27 monomethylation at specific sites, thereby leading to closed heterochromatin states and transcriptional silencing.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2300-2318"},"PeriodicalIF":13.6,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02137-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145357949","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}
Pub Date : 2025-10-24DOI: 10.1038/s41477-025-02130-6
Guang-Jiu Hao, Fei Yu, Zi-zhen Liang, Le-Yan Su, Xin-Ying Zhao, Gui-Min Yin, Sha Li, Yan Zhang
The establishment of polarity is an evolutionarily recurring theme in all eukaryotes. Pollen germination in angiosperms establishes polarity, which is critical for reproduction and a barrier for inter-species crosses. Arabidopsis Rho of plants (ROPs) and their guanine nucleotide exchange factor 8 (RopGEF8) are essential for pollen germination through their polar distribution at the plasma membrane and asymmetric activation of downstream activities. Events leading to the polar plasma membrane association of RopGEF8 and ROPs during pollen germination are yet to be uncovered. We report here that canonical and plant-unique Rab5 GTPases, regulators of vesicular trafficking, synergistically regulate pollen germination. Intriguingly, the role of Rab5s in this process is independent of their own GEFs. Instead, Rab5 GTPases directly interact with RopGEF8 in an activity-independent way and mediate its polar plasma membrane targeting from endosomes. Our finding that Rab5 GTPases influence ROP signalling through RopGEF8 suggests an evolutionary innovation by plants. By using the combination of both canonical and plant-unique Rab5 GTPases, ROP signalling can be regulated in a more delicate manner. Consequently, various internal and external inputs are interpreted to ensure the proper timing of pollen germination. Rab5 GTPases deliver RopGEF8 from endosomes to the pollen plasma membrane, establishing polarity for germination. This crosstalk between trafficking and signalling GTPases is crucial for the reproductive success of flowering plants.
{"title":"Rab5 GTPases mediate the targeting of ROP signalling to establish polarity for pollen germination","authors":"Guang-Jiu Hao, Fei Yu, Zi-zhen Liang, Le-Yan Su, Xin-Ying Zhao, Gui-Min Yin, Sha Li, Yan Zhang","doi":"10.1038/s41477-025-02130-6","DOIUrl":"10.1038/s41477-025-02130-6","url":null,"abstract":"The establishment of polarity is an evolutionarily recurring theme in all eukaryotes. Pollen germination in angiosperms establishes polarity, which is critical for reproduction and a barrier for inter-species crosses. Arabidopsis Rho of plants (ROPs) and their guanine nucleotide exchange factor 8 (RopGEF8) are essential for pollen germination through their polar distribution at the plasma membrane and asymmetric activation of downstream activities. Events leading to the polar plasma membrane association of RopGEF8 and ROPs during pollen germination are yet to be uncovered. We report here that canonical and plant-unique Rab5 GTPases, regulators of vesicular trafficking, synergistically regulate pollen germination. Intriguingly, the role of Rab5s in this process is independent of their own GEFs. Instead, Rab5 GTPases directly interact with RopGEF8 in an activity-independent way and mediate its polar plasma membrane targeting from endosomes. Our finding that Rab5 GTPases influence ROP signalling through RopGEF8 suggests an evolutionary innovation by plants. By using the combination of both canonical and plant-unique Rab5 GTPases, ROP signalling can be regulated in a more delicate manner. Consequently, various internal and external inputs are interpreted to ensure the proper timing of pollen germination. Rab5 GTPases deliver RopGEF8 from endosomes to the pollen plasma membrane, establishing polarity for germination. This crosstalk between trafficking and signalling GTPases is crucial for the reproductive success of flowering plants.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2319-2331"},"PeriodicalIF":13.6,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145357952","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}
Pub Date : 2025-10-20DOI: 10.1038/s41477-025-02149-9
All over the world, farmers are finding new ways to adapt to climate change. But these innovations risk severing connections to the land that have been shaped over millennia.
{"title":"Old crops in new places","authors":"","doi":"10.1038/s41477-025-02149-9","DOIUrl":"10.1038/s41477-025-02149-9","url":null,"abstract":"All over the world, farmers are finding new ways to adapt to climate change. But these innovations risk severing connections to the land that have been shaped over millennia.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 10","pages":"1977-1978"},"PeriodicalIF":13.6,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02149-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327833","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}
Fruit ripening is a tightly regulated developmental process, in which nuclear gene transcription represents a crucial component of the mechanisms1. Chloroplast-associated protein degradation, a recently discovered pathway for chloroplast protein degradation, has also been reported to control fruit ripening2. Here we report a negative regulator of tomato ripening, termed SlSAD8, which disturbs both nuclear gene transcription and chloroplast-associated protein degradation. As an atypical stearoyl-ACP desaturase (SAD) protein exhibiting dual localization in plastids and the nucleus, SlSAD8 negatively regulates ripening initiation and chloroplast-to-chromoplast transition during fruit ripening. In the nucleus, SlSAD8 interacts with ripening-initiation-associated transcription factor SlNAM1, thereby disturbing the transcriptional activation of ethylene biosynthesis genes. Additionally, SlSAD8 interacts with plastid-transition-associated E3 ligase SlSP1 in the plastid, disturbing the chloroplast-associated protein degradation pathway to elevate chloroplast protein levels. Our findings uncover an unusual ripening regulator that targets distinct subcellular compartments to manipulate gene expression, providing insights into the intricate regulatory networks of fruit ripening. This study reports an unusual tomato ripening regulator, SlSAD8, that targets distinct subcellular compartments to disturb nuclear gene transcription and chloroplast-associated protein degradation, thus uncovering a pathway for fruit ripening.
{"title":"Tomato ripening regulator SlSAD8 disturbs nuclear gene transcription and chloroplast-associated protein degradation","authors":"Chan Xu, Rui Li, Xiaoyan Chen, Zhengyang Fu, Xuechun Cui, Juanni Yao, Yanna Shi, Wei Deng, Zhengguo Li, Yulin Cheng","doi":"10.1038/s41477-025-02134-2","DOIUrl":"10.1038/s41477-025-02134-2","url":null,"abstract":"Fruit ripening is a tightly regulated developmental process, in which nuclear gene transcription represents a crucial component of the mechanisms1. Chloroplast-associated protein degradation, a recently discovered pathway for chloroplast protein degradation, has also been reported to control fruit ripening2. Here we report a negative regulator of tomato ripening, termed SlSAD8, which disturbs both nuclear gene transcription and chloroplast-associated protein degradation. As an atypical stearoyl-ACP desaturase (SAD) protein exhibiting dual localization in plastids and the nucleus, SlSAD8 negatively regulates ripening initiation and chloroplast-to-chromoplast transition during fruit ripening. In the nucleus, SlSAD8 interacts with ripening-initiation-associated transcription factor SlNAM1, thereby disturbing the transcriptional activation of ethylene biosynthesis genes. Additionally, SlSAD8 interacts with plastid-transition-associated E3 ligase SlSP1 in the plastid, disturbing the chloroplast-associated protein degradation pathway to elevate chloroplast protein levels. Our findings uncover an unusual ripening regulator that targets distinct subcellular compartments to manipulate gene expression, providing insights into the intricate regulatory networks of fruit ripening. This study reports an unusual tomato ripening regulator, SlSAD8, that targets distinct subcellular compartments to disturb nuclear gene transcription and chloroplast-associated protein degradation, thus uncovering a pathway for fruit ripening.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2230-2239"},"PeriodicalIF":13.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311245","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}
Pub Date : 2025-10-13DOI: 10.1038/s41477-025-02105-7
César Leblanc, Pierre Bonnet, Maximilien Servajean, Wilfried Thuiller, Milan Chytrý, Svetlana Aćić, Olivier Argagnon, Idoia Biurrun, Gianmaria Bonari, Helge Bruelheide, Juan Antonio Campos, Andraž Čarni, Renata Ćušterevska, Michele De Sanctis, Jürgen Dengler, Tetiana Dziuba, Emmanuel Garbolino, Ute Jandt, Florian Jansen, Jonathan Lenoir, Jesper Erenskjold Moeslund, Aaron Pérez-Haase, Remigiusz Pielech, Jozef Sibik, Zvjezdana Stančić, Domas Uogintas, Thomas Wohlgemuth, Alexis Joly
To address the urgent biodiversity crisis, it is crucial to understand the nature of plant assemblages. The distribution of plant species is shaped not only by their broad environmental requirements but also by micro-environmental conditions, dispersal limitations, and direct and indirect species interactions. While predicting species composition and habitat type is essential for conservation and restoration purposes, it remains challenging. In this study, we propose an approach inspired by advances in large language models to learn the ‘syntax’ of abundance-ordered plant species sequences in communities. Our method, which captures latent associations between species across diverse ecosystems, can be fine-tuned for diverse tasks. In particular, we show that our methodology is able to outperform other approaches to (1) predict species that might occur in an assemblage given the other listed species, despite being originally missing in the species list (16.53% higher accuracy in retrieving a plant species removed from an assemblage than co-occurrence matrices and 6.56% higher than neural networks), and (2) classify habitat types from species assemblages (5.54% higher accuracy in assigning a habitat type to an assemblage than expert system classifiers and 1.14% higher than tabular deep learning). The proposed application has a vocabulary that covers over 10,000 plant species from Europe and adjacent countries and provides a powerful methodology for improving biodiversity mapping, restoration and conservation biology. As ecologists begin to explore the use of artificial intelligence, such approaches open opportunities for rethinking how we model, monitor and understand nature. Pl@ntBERT is a language-based AI model that learned the ‘syntax’ of plant assemblages, predicting likely species and inferring habitats by modelling biotic relationships.
{"title":"Learning the syntax of plant assemblages","authors":"César Leblanc, Pierre Bonnet, Maximilien Servajean, Wilfried Thuiller, Milan Chytrý, Svetlana Aćić, Olivier Argagnon, Idoia Biurrun, Gianmaria Bonari, Helge Bruelheide, Juan Antonio Campos, Andraž Čarni, Renata Ćušterevska, Michele De Sanctis, Jürgen Dengler, Tetiana Dziuba, Emmanuel Garbolino, Ute Jandt, Florian Jansen, Jonathan Lenoir, Jesper Erenskjold Moeslund, Aaron Pérez-Haase, Remigiusz Pielech, Jozef Sibik, Zvjezdana Stančić, Domas Uogintas, Thomas Wohlgemuth, Alexis Joly","doi":"10.1038/s41477-025-02105-7","DOIUrl":"10.1038/s41477-025-02105-7","url":null,"abstract":"To address the urgent biodiversity crisis, it is crucial to understand the nature of plant assemblages. The distribution of plant species is shaped not only by their broad environmental requirements but also by micro-environmental conditions, dispersal limitations, and direct and indirect species interactions. While predicting species composition and habitat type is essential for conservation and restoration purposes, it remains challenging. In this study, we propose an approach inspired by advances in large language models to learn the ‘syntax’ of abundance-ordered plant species sequences in communities. Our method, which captures latent associations between species across diverse ecosystems, can be fine-tuned for diverse tasks. In particular, we show that our methodology is able to outperform other approaches to (1) predict species that might occur in an assemblage given the other listed species, despite being originally missing in the species list (16.53% higher accuracy in retrieving a plant species removed from an assemblage than co-occurrence matrices and 6.56% higher than neural networks), and (2) classify habitat types from species assemblages (5.54% higher accuracy in assigning a habitat type to an assemblage than expert system classifiers and 1.14% higher than tabular deep learning). The proposed application has a vocabulary that covers over 10,000 plant species from Europe and adjacent countries and provides a powerful methodology for improving biodiversity mapping, restoration and conservation biology. As ecologists begin to explore the use of artificial intelligence, such approaches open opportunities for rethinking how we model, monitor and understand nature. Pl@ntBERT is a language-based AI model that learned the ‘syntax’ of plant assemblages, predicting likely species and inferring habitats by modelling biotic relationships.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 10","pages":"2026-2040"},"PeriodicalIF":13.6,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02105-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145283548","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}
Pub Date : 2025-10-10DOI: 10.1038/s41477-025-02111-9
Xiaojing Zhang, Hao Jiang, Guangqi Zhu, Fuhai Chen, Weichao Yuan, Yaqin Li, Wanqing Zhang, Dian Wu, Huili Liu, Hen-Ming Wu, Alice Y. Cheung, Li-Zhen Tao
Auxin plays a critical role throughout plant development. We have established earlier that auxin activates the ROP (plant RHO GTPase) molecular switch, and that guanine nucleotide exchange factors ROPGEFs, which activate ROPs, are important regulators for myriad auxin-regulated processes. Here we show that auxin induces phosphorylation of RopGEF1 and that four receptor-like cytoplasmic kinases (RLCKs), named RopGEF1-activating kinases 1/2/3/4 (RAK1/2/3/4), mediate this process. We show that RAKs interact with RopGEFs and specifically phosphorylate S488 on RopGEF1, promoting its stability and recruitment to the cell membrane, and enhance ROP activation. Knockout of these RLCKs blocked auxin-stimulated RopGEF1 phosphorylation, reduced ROP activation and led to defects in PIN-FORMED (PIN)-mediated auxin distribution and multiple developmental processes. Phospho-mimic RopGEF1 (S488D) shows enhanced guanine nucleotide exchange activity in vitro, and its expression in rak quadruple mutants reverses their phenotypes. The RLCK–RopGEF linkage represents an important functional node and elucidates a critical missing link in ROP-meditated auxin signaling. Four receptor-like cytoplasmic kinases (RLCKs) phosphorylate guanine nucleotide exchange factors (RopGEFs), filling a critical gap in the signalling pathway connecting cell surface auxin and RHO GTPases (ROPs) in Arabidopsis.
生长素在植物发育过程中起着至关重要的作用。我们之前已经证实，生长素激活植物RHO GTPase分子开关，而激活ROP的鸟嘌呤核苷酸交换因子ROPGEFs是生长素调控过程的重要调节因子。本研究表明，生长素诱导RopGEF1磷酸化，四种被称为RopGEF1激活激酶1/2/3/4 （RAK1/2/3/4）的受体样细胞质激酶（RLCKs）介导了这一过程。我们发现RAKs与ropgef相互作用，特异性磷酸化RopGEF1上的S488，促进其稳定性和向细胞膜募集，并增强ROP的激活。敲除这些RLCKs阻断生长素刺激的RopGEF1磷酸化，降低ROP激活，导致PIN- formed （PIN - formed）介导的生长素分布和多种发育过程的缺陷。Phospho-mimic RopGEF1 （S488D）在体外显示出增强的鸟嘌呤核苷酸交换活性，其在rak四重突变体中的表达逆转了其表型。RLCK-RopGEF链接代表了一个重要的功能节点，并阐明了rop介导的生长素信号传导中一个关键的缺失环节。
{"title":"RLCKs phosphorylate RopGEFs to control auxin-dependent Arabidopsis development","authors":"Xiaojing Zhang, Hao Jiang, Guangqi Zhu, Fuhai Chen, Weichao Yuan, Yaqin Li, Wanqing Zhang, Dian Wu, Huili Liu, Hen-Ming Wu, Alice Y. Cheung, Li-Zhen Tao","doi":"10.1038/s41477-025-02111-9","DOIUrl":"10.1038/s41477-025-02111-9","url":null,"abstract":"Auxin plays a critical role throughout plant development. We have established earlier that auxin activates the ROP (plant RHO GTPase) molecular switch, and that guanine nucleotide exchange factors ROPGEFs, which activate ROPs, are important regulators for myriad auxin-regulated processes. Here we show that auxin induces phosphorylation of RopGEF1 and that four receptor-like cytoplasmic kinases (RLCKs), named RopGEF1-activating kinases 1/2/3/4 (RAK1/2/3/4), mediate this process. We show that RAKs interact with RopGEFs and specifically phosphorylate S488 on RopGEF1, promoting its stability and recruitment to the cell membrane, and enhance ROP activation. Knockout of these RLCKs blocked auxin-stimulated RopGEF1 phosphorylation, reduced ROP activation and led to defects in PIN-FORMED (PIN)-mediated auxin distribution and multiple developmental processes. Phospho-mimic RopGEF1 (S488D) shows enhanced guanine nucleotide exchange activity in vitro, and its expression in rak quadruple mutants reverses their phenotypes. The RLCK–RopGEF linkage represents an important functional node and elucidates a critical missing link in ROP-meditated auxin signaling. Four receptor-like cytoplasmic kinases (RLCKs) phosphorylate guanine nucleotide exchange factors (RopGEFs), filling a critical gap in the signalling pathway connecting cell surface auxin and RHO GTPases (ROPs) in Arabidopsis.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 10","pages":"2130-2144"},"PeriodicalIF":13.6,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145261298","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}
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