Molecular Plant最新文献_第2页

Sensing H₂O₂ for defense in plants.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-04 DOI: 10.1016/j.molp.2025.03.004

Yan Bi, Leeza Tariq, Hui Wang, Fengming Song

引用次数: 0

The near-complete genome assembly of pickling cucumber and its mutation library illuminate cucumber functional genomics and genetic improvement.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-04 DOI: 10.1016/j.molp.2025.03.001

Yao Tian, Kui Li, Tonghui Li, Wudi Gai, Jie Zhou, Xing Wang Deng, Yan Xue, Yun Deng, Hang He, Xingping Zhang

引用次数: 0

SuperDecode: an integrated toolkit for analyzing mutations induced by genome editing.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-04 DOI: 10.1016/j.molp.2025.03.002

Fuquan Li, Xiyu Tan, Shengting Li, Shaotong Chen, Lin Liu, Jingjing Huang, Gufeng Li, Zijun Lu, Jingwen Wu, Dongchang Zeng, Yanqiu Luo, Xiaoou Dong, Xingliang Ma, Qinlong Zhu, Letian Chen, Yao-Guang Liu, Chengjie Chen, Xianrong Xie

{"title":"SuperDecode: an integrated toolkit for analyzing mutations induced by genome editing.","authors":"Fuquan Li, Xiyu Tan, Shengting Li, Shaotong Chen, Lin Liu, Jingjing Huang, Gufeng Li, Zijun Lu, Jingwen Wu, Dongchang Zeng, Yanqiu Luo, Xiaoou Dong, Xingliang Ma, Qinlong Zhu, Letian Chen, Yao-Guang Liu, Chengjie Chen, Xianrong Xie","doi":"10.1016/j.molp.2025.03.002","DOIUrl":"https://doi.org/10.1016/j.molp.2025.03.002","url":null,"abstract":"Genome editing using CRISPR/Cas or other systems has become a cornerstone of numerous biological and applied research fields. However, detecting the resulting mutations by analysis of sequencing data remains time-consuming and inefficient. In response to this issue, we designed SuperDecode, an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies. SuperDecode comprises three modules, DSDecodeMS, HiDecode, and LaDecode, each designed to automatically decode mutations from Sanger, high-throughput short-read (next-generation sequencing), and long-read sequencing data (third-generation sequencing), respectively, from targeted PCR amplicons. By leveraging specific strategies for constructing sequencing libraries of pooled multiple amplicons, HiDecode and LaDecode facilitate large-scale identification of mutations induced by single or multiplex target-site editing in a cost-effective manner. We demonstrate the efficacy of SuperDecode by analyzing mutations produced using different genome editing tools (CRISPR/Cas, base editing, prime editing) in different materials (diploid and tetraploid rice, protoplasts), underscoring its versatility in decoding genome editing outcomes across different applications. Furthermore, this toolkit can be used to analyze other genetic variations, as exemplified by its ability to estimate the C-to-U editing rate of the cellular RNA of a mitochondrial gene. SuperDecode offers both a standalone software package and a web-based version, ensuring its easy access and broad compatibility across diverse computer systems. Thus, SuperDecode provides a comprehensive platform for analyzing a wide array of mutations, advancing the utility of genome editing for scientific research and genetic engineering.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567749","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

DNA damage triggers heritable alterations in DNA methylation patterns in Arabidopsis. DNA损伤引发拟南芥DNA甲基化模式的遗传改变

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-24 DOI: 10.1016/j.molp.2025.01.019

Jinchao Li, Wenjie Liang, Xin-Qiang He, Weiqiang Qian

{"title":"DNA damage triggers heritable alterations in DNA methylation patterns in Arabidopsis.","authors":"Jinchao Li, Wenjie Liang, Xin-Qiang He, Weiqiang Qian","doi":"10.1016/j.molp.2025.01.019","DOIUrl":"10.1016/j.molp.2025.01.019","url":null,"abstract":"It has been hypothesized that DNA damage has the potential to induce DNA hypermethylation, contributing to carcinogenesis in mammals. However, there is no sufficient evidence to support that DNA damage can cause genome-wide DNA hypermethylation. In this study, we demonstrated that DNA single-strand breaks with 3' blocked ends (DNA 3' blocks) not only can reinforce DNA methylation at normally methylated loci but also can induce DNA methylation at normally nonmethylated loci in plants. The CG and CHG hypermethylation tend to localize within gene bodies, with a significant proportion being de novo generated. In contrast, the CHH hypermethylation is concentrated in centromeric and pericentromeric regions, primarily being reinforced methylation. Mechanistically, DNA 3' blocks regulate the DREAM complex to induce CG and CHG methylation. Moreover, they utilize the RdDM pathway to induce CHH hypermethylation. Intriguingly, repair of DNA damage or blocking the DNA damage response can fully abolish CHH hypermethylation and partially rescue CHG hypermethylation but rarely alter CG hypermethylation, indicating that DNA damage-induced symmetric DNA methylation can serve as a form of genetic imprinting. Collectively, these results suggest that DNA damage is an important force driving the emergence and evolution of genomic DNA methylation levels and patterns in plants.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"501-512"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040166","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

The plant retromer components SNXs bind to ATG8 and CLASP to mediate autophagosome movement along microtubules. 植物逆转录成分SNXs与ATG8和CLASP结合介导自噬体沿微管运动。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2024-12-24 DOI: 10.1016/j.molp.2024.12.013

Yanglan Liao, Xibao Li, Wenlong Ma, Xinyi Lin, Jiayi Kuang, Xuanang Zheng, Zien Li, Fanfan Qiao, Chuanliang Liu, Jun Zhou, Faqiang Li, Ruixi Li, Byung-Ho Kang, Hongbo Li, Caiji Gao

{"title":"The plant retromer components SNXs bind to ATG8 and CLASP to mediate autophagosome movement along microtubules.","authors":"Yanglan Liao, Xibao Li, Wenlong Ma, Xinyi Lin, Jiayi Kuang, Xuanang Zheng, Zien Li, Fanfan Qiao, Chuanliang Liu, Jun Zhou, Faqiang Li, Ruixi Li, Byung-Ho Kang, Hongbo Li, Caiji Gao","doi":"10.1016/j.molp.2024.12.013","DOIUrl":"10.1016/j.molp.2024.12.013","url":null,"abstract":"In eukaryotic cells, autophagosomes are double-membrane vesicles that are highly mobile and traffic along cytoskeletal tracks. While core autophagy-related proteins (ATGs) and other regulators involved in autophagosome biogenesis in plants have been extensively studied, the specific components regulating plant autophagosome motility remain elusive. In this study, using TurboID-based proximity labeling, we identify the retromer subcomplex comprising sorting nexin 1 (SNX1), SNX2a, and SNX2b as interacting partners of ATG8. Remarkably, SNX proteins decorate ATG8-labeled autophagosomes and facilitate their coordinated movement along microtubules. Depletion of SNX proteins restricts the motility of autophagosomes in the cytoplasm, resulting in decreased autophagic flux. Furthermore, we show that the microtubule-associated protein CLASP is a bridge, connecting the SNX-ATG8-decorated autophagosomes to the microtubules. Genetically, the clasp-1 mutant phenotype resembles that of plants with disrupted SNXs or microtubule networks, displaying diminished autophagosome motility and reduced autophagic flux. Collectively, our study unveils a hitherto unanticipated role of the SNXs subcomplex in connecting autophagosomes with microtubules to promote autophagosome mobility in Arabidopsis.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"416-436"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885951","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

Reevaluating statistical methods in metabolomic studies: A case for Spearman's correlation. 代谢组学研究中统计方法的重新评估：一个Spearman相关的案例。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2024-12-24 DOI: 10.1016/j.molp.2024.12.014

Yoshiyasu Takefuji

引用次数: 0

Activation and memory of the heat shock response is mediated by prion-like domains of sensory HSFs in Arabidopsis. 拟南芥热休克反应的激活和记忆是由感觉hsf的朊蛋白样结构域介导的。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-09 DOI: 10.1016/j.molp.2025.01.007

Maolin Peng, Katja E Jaeger, Yunlong Lu, Zhuping Fan, Wei Zeng, Arun Sampathkumar, Philip A Wigge

{"title":"Activation and memory of the heat shock response is mediated by prion-like domains of sensory HSFs in Arabidopsis.","authors":"Maolin Peng, Katja E Jaeger, Yunlong Lu, Zhuping Fan, Wei Zeng, Arun Sampathkumar, Philip A Wigge","doi":"10.1016/j.molp.2025.01.007","DOIUrl":"10.1016/j.molp.2025.01.007","url":null,"abstract":"Plants are able to sense and remember heat stress. An initial priming heat stress enables plants to acclimate so that they are able to survive a subsequent higher temperature. The heat shock transcription factors (HSFs) play a crucial role in this process, but the mechanisms by which plants sense heat stress are not well understood. By comprehensively analyzing the binding targets of all the HSFs, we found that HSFs act in a network, with upstream sensory HSFs acting in a transcriptional cascade to activate downstream HSFs and protective proteins. The upstream sensory HSFs are activated by heat at the protein level via a modular prion-like domain (PrD) structure. PrD1 enables HSF sequestration via chaperone binding, allowing release under heat shock. Activated HSFs are recruited into transcriptionally active foci via PrD2, enabling the formation of DNA loops between heat-responsive promoters and enhancer motifs, boosting gene expression days after a priming heat stress. The ability of HSFs to respond rapidly to heat via a protein phase-change response is likely a conserved mechanism in eukaryotes.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"457-467"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142952128","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

GEFormer: A genotype-environment interaction-based genomic prediction method that integrates the gating multilayer perceptron and linear attention mechanisms.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-28 DOI: 10.1016/j.molp.2025.01.020

Zhou Yao, Mengting Yao, Chuang Wang, Ke Li, Junhao Guo, Yingjie Xiao, Jianbing Yan, Jianxiao Liu

{"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":"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.","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}

引用次数: 0

Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid. 基因组学、转录组学和代谢组学分析揭示了达尔文兰花的肟生物合成趋同进化。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2024-12-18 DOI: 10.1016/j.molp.2024.12.010

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

{"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":"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.","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}

引用次数: 0

Chloroplast state transitions modulate nuclear genome stability via cytokinin signaling in Arabidopsis.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-28 DOI: 10.1016/j.molp.2025.01.021

Yajun Zeng, Sujuan Duan, Yawen Wang, Zhifeng Zheng, Zeyi Wu, Meihui Shi, Manchun Wang, Lan Jiang, Xue Li, Hong-Bin Wang, Hong-Lei Jin

{"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":"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.","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}

引用次数: 0