Nature Plants最新文献

{"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}

{"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":"https://doi.org/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.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"101 1","pages":""},"PeriodicalIF":18.0,"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}

{"title":"Nitrate to spark parched plants.","authors":"Justine Broutin, Christian Meyer","doi":"10.1038/s41477-025-02150-2","DOIUrl":"https://doi.org/10.1038/s41477-025-02150-2","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308349","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":"Deconstructing soybean domestication","authors":"Jun Lyu","doi":"10.1038/s41477-025-02143-1","DOIUrl":"10.1038/s41477-025-02143-1","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 10","pages":"1982-1982"},"PeriodicalIF":13.6,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145302039","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":"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}

{"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}

{"title":"Pan-centromere landscape and dynamic evolution in Brassica plants.","authors":"Weikai Chen,Jingxuan Wang,Shaoying Chen,Dian Meng,Yu Mu,Hui Feng,Lugang Zhang,Li Guo","doi":"10.1038/s41477-025-02131-5","DOIUrl":"https://doi.org/10.1038/s41477-025-02131-5","url":null,"abstract":"The centromere paradox, in which functionally conserved centromeres exhibit rapid evolution, has long intrigued geneticists and evolutionary biologists. Despite its importance, the centromeric landscape remains poorly understood due to the lack of complete assemblies. Here we dissect the dynamic evolution of Brassica centromeres by generating telomere-to-telomere genome assemblies from seven morphotypes of B. rapa (AA) and the two tetraploids B. juncea (AABB) and B. napus (AACC). Pan-centromere analysis reveals that Brassica centromeres are extensively invaded by retrotransposons and show remarkable diversity in size and structure. While A- and C-genome centromeres feature distinct patterns of satellites, B-genome centromeres are devoid of satellites. The centromeric satellite expansion in the C-genome is reminiscent of the layered expansions observed in human centromeres. Accordingly, we propose a working model of centromere evolution reconstructing the key evolutionary events leading to current Brassica centromere structures. These insights will illuminate plant centromere evolution and guide the design of crop synthetic chromosomes.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"40 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145261280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The chloroplast-targeted long noncoding RNA CHLORELLA mediates chloroplast functional transition across leaf ageing via anterograde signalling.","authors":"Myeong Hoon Kang,Juhyeon Lee,Jinkwang Kim,Hazara Begum Mohammad,Jeehye Park,Hyun Ju Jung,Seonghwan Kim,Heeho Lee,Seong Wook Yang,June M Kwak,Min-Sik Kim,Jong-Chan Lee,Pyung Ok Lim","doi":"10.1038/s41477-025-02129-z","DOIUrl":"https://doi.org/10.1038/s41477-025-02129-z","url":null,"abstract":"The transition from chloroplast biogenesis to degeneration during leaf senescence is critical for plants' fitness, as it facilitates the relocation of nutrients to reproductive organs1-3. However, it remains largely unknown how the timing of this transition is regulated by the coordination between chloroplasts and the nucleus4,5. Here we describe the regulatory mechanism underlying this transition in Arabidopsis thaliana. CHLOROPLAST-RELATED LONG NONCODING RNA (CHLORELLA) is highly co-expressed with genes supporting chloroplast function during leaf development. Leaves lacking CHLORELLA exhibit precocious senescence and reduced expression of chloroplast-associated genes, suggesting that CHLORELLA helps maintain chloroplast function. Mechanistically, CHLORELLA transcripts are translocated into chloroplasts and contribute to the accumulation of the plastid-encoded RNA polymerase complex. As leaves age, the expression of CHLORELLA decreases, leading to reduced plastid-encoded RNA polymerase accumulation and diminished transcription of photosynthesis-related genes, which may trigger leaf senescence. Moreover, CHLORELLA expression is activated by GOLDEN2-LIKE1 and GOLDEN2-LIKE2, master regulators of chloroplast development6-8. Our study unravels a long-noncoding-RNA-based anterograde signalling mechanism that facilitates timely leaf senescence.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"72 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145261287","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":"Cambium curbed by RABBIT EARS","authors":"Raphael Trösch","doi":"10.1038/s41477-025-02144-0","DOIUrl":"10.1038/s41477-025-02144-0","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 10","pages":"1981-1981"},"PeriodicalIF":13.6,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251902","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":"MAIL proteins prevent Polycomb silencing to keep genes active.","authors":"","doi":"10.1038/s41477-025-02132-4","DOIUrl":"https://doi.org/10.1038/s41477-025-02132-4","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"12 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145241086","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}