Nature Plants最新文献_第2页

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-16 DOI: 10.1038/s41477-025-01904-2

Raphael Trösch

引用次数: 0

Convergent reduction of immune receptor repertoires during plant adaptation to diverse special lifestyles and habitats 植物适应不同特殊生活方式和栖息地过程中免疫受体的趋同性降低

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-16 DOI: 10.1038/s41477-024-01901-x

Sai-Xi Li, Yang Liu, Yan-Mei Zhang, Jian-Qun Chen, Zhu-Qing Shao

{"title":"Convergent reduction of immune receptor repertoires during plant adaptation to diverse special lifestyles and habitats","authors":"Sai-Xi Li, Yang Liu, Yan-Mei Zhang, Jian-Qun Chen, Zhu-Qing Shao","doi":"10.1038/s41477-024-01901-x","DOIUrl":"https://doi.org/10.1038/s41477-024-01901-x","url":null,"abstract":"Plants deploy cell-surface pattern recognition receptors (PRRs) and intracellular nucleotide-binding site–leucine-rich repeat receptors (NLRs) to recognize pathogens. However, how plant immune receptor repertoires evolve in responding to changed pathogen burdens remains elusive. Here we reveal the convergent reduction of NLR repertoires in plants with diverse special lifestyles/habitats (SLHs) encountering low pathogen burdens. Furthermore, a parallel but milder reduction of PRR genes in SLH species was observed. The reduction of PRR and NLR genes was attributed to both increased gene loss and decreased gene duplication. Notably, pronounced loss of immune receptors was associated with the complete absence of signalling components from the enhanced disease susceptibility 1 (EDS1) and the resistance to powdery mildew 8 (RPW8)-NLR (RNL) families. In addition, evolutionary pattern analysis suggested that the conserved toll/interleukin-1 receptor (TIR)-only proteins might function tightly with EDS1/RNL. Taken together, these results reveal the hierarchically adaptive evolution of the two-tiered immune receptor repertoires during plant adaptation to diverse SLHs.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"95 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142986186","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}

引用次数: 0

Molecular regulation and domestication of parthenocarpy in cucumber 黄瓜孤雌核的分子调控与驯化

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-15 DOI: 10.1038/s41477-024-01899-2

Jing Nie, Hongyu Huang, Sheng Wu, Tao Lin, Lidong Zhang, Lijun Lv, Yuzi Shi, Yicong Guo, Qian Zhang, Yuhe Li, Weiliang Kong, Hujian Li, Zhen Yang, Wenbo Li, Lingjun Xu, Nan Ma, Zhonghua Zhang, Chuanqing Sun, Xiaolei Sui

{"title":"Molecular regulation and domestication of parthenocarpy in cucumber","authors":"Jing Nie, Hongyu Huang, Sheng Wu, Tao Lin, Lidong Zhang, Lijun Lv, Yuzi Shi, Yicong Guo, Qian Zhang, Yuhe Li, Weiliang Kong, Hujian Li, Zhen Yang, Wenbo Li, Lingjun Xu, Nan Ma, Zhonghua Zhang, Chuanqing Sun, Xiaolei Sui","doi":"10.1038/s41477-024-01899-2","DOIUrl":"https://doi.org/10.1038/s41477-024-01899-2","url":null,"abstract":"Parthenocarpy is a pivotal trait that enhances the yield and quality of fruit crops by enabling the development of seedless fruits. Here we unveil a molecular framework for the regulation and domestication of parthenocarpy in cucumber (Cucumis sativus L.). We previously discovered a natural non-parthenocarpic mutant and demonstrated that the AP2-like transcription factor NON-PARTHENOCARPIC FRUIT 1 (NPF1) is a central regulator of parthenocarpy through activating YUC4 expression and promoting auxin biosynthesis in ovules. A Phe-to-Ser substitution at amino acid residue 7 results in a stable form of NPF1 that is localized in the nucleus. An A-to-G polymorphism (SNP-383) within an NPF1-binding site in the YUC4 promoter significantly enhances the activation of NPF1 towards YUC4, leading to an increased rate of parthenocarpy. Additionally, NPF1 influences bitterness by reducing cucurbitacin C biosynthesis through the suppression of Bt expression. Our results suggest a two-step evolutionary model for parthenocarpy and fruit bitterness during cucumber domestication.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"23 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981349","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}

引用次数: 0

Precise deletion, replacement and inversion of large DNA fragments in plants using dual prime editing 利用双引物编辑在植物中精确地删除、替换和反转大的DNA片段

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-13 DOI: 10.1038/s41477-024-01898-3

Yidi Zhao, Zhengwei Huang, Ximeng Zhou, Wan Teng, Zehua Liu, Wenping Wang, Shengjia Tang, Ying Liu, Jing Liu, Wenxi Wang, Lingling Chai, Na Zhang, Weilong Guo, Jie Liu, Zhongfu Ni, Qixin Sun, Yanpeng Wang, Yuan Zong

{"title":"Precise deletion, replacement and inversion of large DNA fragments in plants using dual prime editing","authors":"Yidi Zhao, Zhengwei Huang, Ximeng Zhou, Wan Teng, Zehua Liu, Wenping Wang, Shengjia Tang, Ying Liu, Jing Liu, Wenxi Wang, Lingling Chai, Na Zhang, Weilong Guo, Jie Liu, Zhongfu Ni, Qixin Sun, Yanpeng Wang, Yuan Zong","doi":"10.1038/s41477-024-01898-3","DOIUrl":"https://doi.org/10.1038/s41477-024-01898-3","url":null,"abstract":"Precise manipulation of genome structural variations holds great potential for plant trait improvement and biological research. Here we present a genome-editing approach, dual prime editing (DualPE), that efficiently facilitates precise deletion, replacement and inversion of large DNA fragments in plants. In our experiments, DualPE enabled the production of specific genomic deletions ranging from ~500 bp to 2 Mb in wheat protoplasts and plants. DualPE was effective in directly replacing wheat genomic fragments of up to 258 kb with desired sequences in the absence of donor DNA. Additionally, DualPE allowed precise DNA inversions of up to 205.4 kb in wheat plants with efficiencies of up to 51.5%. DualPE also successfully edited large DNA fragments in the dicots Nicotiana benthamiana and tomato, with editing efficiencies of up to 72.7%. DualPE thus provides a precise and efficient approach for large DNA sequence and chromosomal engineering, expanding the availability of precision genome-editing tools for crop improvement.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"54 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968264","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}

引用次数: 0

Tomato fruit ripening is modulated by redox modification of RNA demethylase 番茄果实成熟是由RNA去甲基酶的氧化还原修饰调控的

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-10 DOI: 10.1038/s41477-024-01900-y

引用次数: 0

Redox modification of m6A demethylase SlALKBH2 in tomato regulates fruit ripening 番茄m6A去甲基化酶SlALKBH2的氧化还原修饰调控果实成熟

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-10 DOI: 10.1038/s41477-024-01893-8

Leilei Zhou, Guangtong Gao, Renkun Tang, Jinying Liu, Yuying Wang, Zhenchang Liang, Shiping Tian, Guozheng Qin

{"title":"Redox modification of m6A demethylase SlALKBH2 in tomato regulates fruit ripening","authors":"Leilei Zhou, Guangtong Gao, Renkun Tang, Jinying Liu, Yuying Wang, Zhenchang Liang, Shiping Tian, Guozheng Qin","doi":"10.1038/s41477-024-01893-8","DOIUrl":"https://doi.org/10.1038/s41477-024-01893-8","url":null,"abstract":"Hydrogen peroxide (H2O2) functions as a critical signalling molecule in controlling multiple biological processes. How H2O2 signalling integrates with other regulatory pathways such as epigenetic modification to coordinately regulate plant development remains elusive. Here we report that SlALKBH2, an m6A demethylase required for normal ripening of tomato fruit, is sensitive to oxidative modification by H2O2, which leads to the formation of homodimers mediated by intermolecular disulfide bonds, and Cys39 serves as a key site in this process. The oxidation of SlALKBH2 promotes protein stability and facilitates its function towards the target transcripts including the pivotal ripening gene SlDML2 encoding a DNA demethylase. Furthermore, we demonstrate that the thioredoxin reductase SlNTRC interacts with SlALKBH2 and catalyses its reduction, thereby modulating m6A levels and fruit ripening. Our study establishes a molecular link between H2O2 and m6A methylation and highlights the importance of redox regulation of m6A modifiers in controlling fruit ripening.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"22 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961488","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}

引用次数: 0

Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium 泛基因基因组分析揭示了兰花属石斛的进化和多样性

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-10 DOI: 10.1038/s41477-024-01902-w

Yan Li, Bin Zhang, Songyao Zhang, Chui Eng Wong, Qiqi Liang, Shuai Pang, Yujin Wu, Ming Zhao, Hao Yu

{"title":"Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium","authors":"Yan Li, Bin Zhang, Songyao Zhang, Chui Eng Wong, Qiqi Liang, Shuai Pang, Yujin Wu, Ming Zhao, Hao Yu","doi":"10.1038/s41477-024-01902-w","DOIUrl":"https://doi.org/10.1038/s41477-024-01902-w","url":null,"abstract":"Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. Here we construct and analyse chromosome-scale de novo assembled genomes of 17 representative accessions spanning 12 sections in Dendrobium, one of the largest orchid genera. These accessions represent a broad spectrum of phenotypes, lineages and geographical distributions. We first construct haplotype-resolved genomes for a Dendrobium hybrid and uncover haplotypic variations and allelic imbalance in the heterozygous genome, demonstrating the significance of diverse ancestry. At Dendrobium genus-wide scale, we further elucidate phylogenetic relationships, evolutionary dynamics, entire gene repertoire, and the mechanisms of preserving ancient genetic variants and rapid recent genome evolution for habitat adaption. We also showcase distinctive evolutionary trajectories in MADS-box and PEBP families over 28 Ma. These results considerably contribute to unearthing the mystery of orchid origin, evolution and diversification, laying the foundation for efficient use of genetic diversity in breeding.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"16 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961491","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}

引用次数: 0

Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation 定量RNA伪尿嘧啶图谱揭示了植物rRNA、tRNA和mRNA伪尿嘧啶化介导的多层次翻译控制

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-09 DOI: 10.1038/s41477-024-01894-7

Haoxuan Li, Guanqun Wang, Chang Ye, Zhongyu Zou, Bochen Jiang, Fan Yang, Kayla He, Chengwei Ju, Lisheng Zhang, Boyang Gao, Shun Liu, Yanming Chen, Jianhua Zhang, Chuan He

{"title":"Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation","authors":"Haoxuan Li, Guanqun Wang, Chang Ye, Zhongyu Zou, Bochen Jiang, Fan Yang, Kayla He, Chengwei Ju, Lisheng Zhang, Boyang Gao, Shun Liu, Yanming Chen, Jianhua Zhang, Chuan He","doi":"10.1038/s41477-024-01894-7","DOIUrl":"https://doi.org/10.1038/s41477-024-01894-7","url":null,"abstract":"Pseudouridine (Ψ) is the most abundant RNA modification, yet studies of Ψ have been hindered by a lack of robust methods to profile comprehensive Ψ maps. Here we utilize bisulfite-induced deletion sequencing to generate transcriptome-wide Ψ maps at single-base resolution across various plant species. Integrating ribosomal RNA, transfer RNA and messenger RNA Ψ stoichiometry with mRNA abundance and polysome profiling data, we uncover a multilayered regulation of translation efficiency through Ψ modifications. rRNA pseudouridylation could globally control translation, although the effects vary at different rRNA Ψ sites. Ψ in the tRNA T-arm loop shows strong positive correlations between Ψ stoichiometry and the translation efficiency of their respective codons. We observed a general inverse correlation between Ψ level and mRNA stability, but a positive correlation with translation efficiency in Arabidopsis seedlings. In conclusion, our study provides critical resources for Ψ research in plants and proposes prevalent translation regulation through rRNA, tRNA and mRNA pseudouridylation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"82 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142936964","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}

引用次数: 0

Small molecules unlock broad-spectrum plant resistance 小分子解开了植物的广谱抗性

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-06 DOI: 10.1038/s41477-024-01891-w

Kaihuai Li, Yan Qiao, Huan Chen, Fengquan Liu

引用次数: 0

Deciphering the core shunt mechanism in Arabidopsis cuticular wax biosynthesis and its role in plant environmental adaptation 拟南芥表皮蜡质生物合成核心分流机制及其在植物环境适应中的作用

IF 18 1区生物学

Nature Plants Pub Date : 2025-01-03 DOI: 10.1038/s41477-024-01892-9

Shipeng Li, Xuanhao Zhang, Haodong Huang, Mou Yin, Matthew A. Jenks, Dylan K. Kosma, Pingfang Yang, Xianpeng Yang, Huayan Zhao, Shiyou Lü

{"title":"Deciphering the core shunt mechanism in Arabidopsis cuticular wax biosynthesis and its role in plant environmental adaptation","authors":"Shipeng Li, Xuanhao Zhang, Haodong Huang, Mou Yin, Matthew A. Jenks, Dylan K. Kosma, Pingfang Yang, Xianpeng Yang, Huayan Zhao, Shiyou Lü","doi":"10.1038/s41477-024-01892-9","DOIUrl":"https://doi.org/10.1038/s41477-024-01892-9","url":null,"abstract":"Plant cuticular waxes serve as highly responsive adaptations to variable environments1,2,3,4,5,6,7. Aliphatic waxes consist of very-long-chain (VLC) compounds produced from 1-alcohol- or alkane-forming pathways5,8. The existing variation in 1-alcohols and alkanes across Arabidopsis accessions revealed that 1-alcohol amounts are negatively correlated with aridity factors, whereas alkanes display the opposite behaviour. How carbon resources are allocated between the 1-alcohol and alkane pathways responding to environmental stimuli is still largely unknown. Here, in Arabidopsis, we report a novel 1-alcohol biosynthesis pathway in which VLC acyl-CoAs are first reduced to aldehydes by CER3 and then converted into 1-alcohols via a newly identified putative aldehyde reductase SOH1. CER3, previously shown to interact with CER1 in alkane synthesis, is identified to interact with SOH1 as well, channelling wax precursors into either alcohol- or alkane-forming pathways, and the directional shunting of these precursors is tightly regulated by the SOH1–CER3–CER1 module in response to environmental conditions.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"20 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917280","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}

引用次数: 0