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WTV2.0: A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode. WTV2.0：具有综合选择性离子监测采集模式的高覆盖率植物挥发物组学方法。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-06-03 Epub Date: 2024-04-29 DOI: 10.1016/j.molp.2024.04.012
Honglun Yuan, Yiding Jiangfang, Zhenhuan Liu, Rongxiu Su, Qiao Li, Chuanying Fang, Sishu Huang, Xianqing Liu, Alisdair R Fernie, Jie Luo
{"title":"WTV2.0: A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode.","authors":"Honglun Yuan, Yiding Jiangfang, Zhenhuan Liu, Rongxiu Su, Qiao Li, Chuanying Fang, Sishu Huang, Xianqing Liu, Alisdair R Fernie, Jie Luo","doi":"10.1016/j.molp.2024.04.012","DOIUrl":"10.1016/j.molp.2024.04.012","url":null,"abstract":"<p><p>Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles. However, the annotation coverage achieved using current untargeted and widely targeted volatomics (WTV) methods has been limited by low sensitivity and/or low acquisition coverage. Here, we introduce WTV 2.0, which enabled the construction of a high-coverage library containing 2111 plant volatiles, and report the development of a comprehensive selective ion monitoring (cSIM) acquisition method, including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method, that can acquire the smallest but sufficient number of ions for most plant volatiles, as well as the automatic qualitative and semi-quantitative analysis of cSIM data. Importantly, the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library, utilizing the obtained cSIM data. We showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method, doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit, and led to the discovery of menthofuran as a novel flavor compound in passion fruit. WTV 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140859824","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 super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. 杨树的超级泛基因组揭示了广泛分布的林木适应和多样化的基因组面貌。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-05-06 Epub Date: 2024-03-13 DOI: 10.1016/j.molp.2024.03.009
Tingting Shi, Xinxin Zhang, Yukang Hou, Changfu Jia, Xuming Dan, Yulin Zhang, Yuanzhong Jiang, Qiang Lai, Jiajun Feng, Jianju Feng, Tao Ma, Jiali Wu, Shuyu Liu, Lei Zhang, Zhiqin Long, Liyang Chen, Nathaniel R Street, Pär K Ingvarsson, Jianquan Liu, Tongming Yin, Jing Wang
{"title":"The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.","authors":"Tingting Shi, Xinxin Zhang, Yukang Hou, Changfu Jia, Xuming Dan, Yulin Zhang, Yuanzhong Jiang, Qiang Lai, Jiajun Feng, Jianju Feng, Tao Ma, Jiali Wu, Shuyu Liu, Lei Zhang, Zhiqin Long, Liyang Chen, Nathaniel R Street, Pär K Ingvarsson, Jianquan Liu, Tongming Yin, Jing Wang","doi":"10.1016/j.molp.2024.03.009","DOIUrl":"10.1016/j.molp.2024.03.009","url":null,"abstract":"<p><p>Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140132080","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 immunity: A cornerstone of plant defense. 叶绿体免疫：植物防御的基石。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-05-06 Epub Date: 2024-03-19 DOI: 10.1016/j.molp.2024.03.012
Jie Liu, Pan Gong, Ruobin Lu, Rosa Lozano-Durán, Xueping Zhou, Fangfang Li
{"title":"Chloroplast immunity: A cornerstone of plant defense.","authors":"Jie Liu, Pan Gong, Ruobin Lu, Rosa Lozano-Durán, Xueping Zhou, Fangfang Li","doi":"10.1016/j.molp.2024.03.012","DOIUrl":"10.1016/j.molp.2024.03.012","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175605","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
Efficient scar-free knock-ins of several kilobases in plants by engineered CRISPR-Cas endonucleases. 通过工程化的 CRISPR/Cas 内切酶，在植物中高效无痕地敲入几千个碱基。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-05-06 Epub Date: 2024-03-22 DOI: 10.1016/j.molp.2024.03.013
Tom Schreiber, Anja Prange, Petra Schäfer, Thomas Iwen, Ramona Grützner, Sylvestre Marillonnet, Aurélie Lepage, Marie Javelle, Wyatt Paul, Alain Tissier
{"title":"Efficient scar-free knock-ins of several kilobases in plants by engineered CRISPR-Cas endonucleases.","authors":"Tom Schreiber, Anja Prange, Petra Schäfer, Thomas Iwen, Ramona Grützner, Sylvestre Marillonnet, Aurélie Lepage, Marie Javelle, Wyatt Paul, Alain Tissier","doi":"10.1016/j.molp.2024.03.013","DOIUrl":"10.1016/j.molp.2024.03.013","url":null,"abstract":"<p><p>In plants and mammals, non-homologous end-joining is the dominant pathway to repair DNA double-strand breaks, making it challenging to generate knock-in events. In this study, we identified two groups of exonucleases from the herpes virus and the bacteriophage T7 families that conferred an up to 38-fold increase in homology-directed repair frequencies when fused to Cas9/Cas12a in a tobacco mosaic virus-based transient assay in Nicotiana benthamiana. We achieved precise and scar-free insertion of several kilobases of DNA both in transient and stable transformation systems. In Arabidopsis thaliana, fusion of Cas9 to a herpes virus family exonuclease led to 10-fold higher frequencies of knock-ins in the first generation of transformants. In addition, we demonstrated stable and heritable knock-ins in wheat in 1% of the primary transformants. Taken together, our results open perspectives for the routine production of heritable knock-in and gene replacement events in plants.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140194232","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
BambooBase: A comprehensive database of bamboo omics and systematics. BambooBase：竹子奥米特和系统学综合数据库。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-05-06 Epub Date: 2024-02-27 DOI: 10.1016/j.molp.2024.02.017
Yun-Long Liu, Shu-Yang Gao, Guihua Jin, Meng-Yuan Zhou, Qijuan Gao, Cen Guo, Yi-Zhou Yang, Liang-Zhong Niu, Enhua Xia, Zhen-Hua Guo, Peng-Fei Ma, De-Zhu Li
{"title":"BambooBase: A comprehensive database of bamboo omics and systematics.","authors":"Yun-Long Liu, Shu-Yang Gao, Guihua Jin, Meng-Yuan Zhou, Qijuan Gao, Cen Guo, Yi-Zhou Yang, Liang-Zhong Niu, Enhua Xia, Zhen-Hua Guo, Peng-Fei Ma, De-Zhu Li","doi":"10.1016/j.molp.2024.02.017","DOIUrl":"10.1016/j.molp.2024.02.017","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139990717","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
Smart Breeding Platform: A web-based tool for high-throughput population genetics, phenomics, and genomic selection. 智能育种平台：基于网络的高通量群体遗传学、表型组学和基因组选择工具。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-05-06 Epub Date: 2024-03-06 DOI: 10.1016/j.molp.2024.03.002
Huihui Li, Xin Li, Peng Zhang, Yingwei Feng, Junri Mi, Shang Gao, Lele Sheng, Mohsin Ali, Zikun Yang, Liang Li, Wei Fang, Wensheng Wang, Qian Qian, Fei Gu, Wenbin Zhou
{"title":"Smart Breeding Platform: A web-based tool for high-throughput population genetics, phenomics, and genomic selection.","authors":"Huihui Li, Xin Li, Peng Zhang, Yingwei Feng, Junri Mi, Shang Gao, Lele Sheng, Mohsin Ali, Zikun Yang, Liang Li, Wei Fang, Wensheng Wang, Qian Qian, Fei Gu, Wenbin Zhou","doi":"10.1016/j.molp.2024.03.002","DOIUrl":"10.1016/j.molp.2024.03.002","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140049972","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
Phosphorus lights up the trade-off between growth and immunity. 磷能在生长和免疫之间做出权衡。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-05-06 Epub Date: 2024-03-29 DOI: 10.1016/j.molp.2024.03.014
Wenyuan Ruan, Meina Guo, Keke Yi
{"title":"Phosphorus lights up the trade-off between growth and immunity.","authors":"Wenyuan Ruan, Meina Guo, Keke Yi","doi":"10.1016/j.molp.2024.03.014","DOIUrl":"10.1016/j.molp.2024.03.014","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140330025","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
Plant RNA-binding proteins: Phase separation dynamics and functional mechanisms underlying plant development and stress responses. 植物 RNA 结合蛋白：植物发育和胁迫响应的相分离动力学和功能机制。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-04-01 Epub Date: 2024-02-27 DOI: 10.1016/j.molp.2024.02.016
Sheng Fan, Yu Zhang, Shaobo Zhu, Lisha Shen
{"title":"Plant RNA-binding proteins: Phase separation dynamics and functional mechanisms underlying plant development and stress responses.","authors":"Sheng Fan, Yu Zhang, Shaobo Zhu, Lisha Shen","doi":"10.1016/j.molp.2024.02.016","DOIUrl":"10.1016/j.molp.2024.02.016","url":null,"abstract":"<p><p>RNA-binding proteins (RBPs) accompany RNA from synthesis to decay, mediating every aspect of RNA metabolism and impacting diverse cellular and developmental processes in eukaryotes. Many RBPs undergo phase separation along with their bound RNA to form and function in dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation of RNA metabolism. Increasing evidence suggests that phase-separating RBPs with RNA-binding domains and intrinsically disordered regions play important roles in plant development and stress adaptation. Here, we summarize the current knowledge about how dynamic partitioning of RBPs into condensates controls plant development and enables sensing of experimental changes to confer growth plasticity under stress conditions, with a focus on the dynamics and functional mechanisms of RBP-rich nuclear condensates and cytoplasmic granules in mediating RNA metabolism. We also discuss roles of multiple factors, such as environmental signals, protein modifications, and N<sup>6</sup>-methyladenosine RNA methylation, in modulating the phase separation behaviors of RBPs, and highlight the prospects and challenges for future research on phase-separating RBPs in crops.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139990718","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
Global wild rice germplasm resources conservation alliance: World Wild-Rice Wiring. 全球野生稻种质资源保护联盟：世界野生稻线路。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-04-01 Epub Date: 2024-03-05 DOI: 10.1016/j.molp.2024.03.001
Xiaoming Zheng, Disna Ratnasekera, Jiayu Fan, Robert J Henry, Beng-Kah Song, Kenneth M Olsen, Bal Krishna Joshi, Maria Celeste N Banaticla-Hilario, Tonapha Pusadee, Adane Getachew Melaku, Yêyinou Laura Estelle Loko, Koukham Vilayheuang, Gavers K Oppong, Samuel Aduse Poku, Peterson W Wambugu, Song Ge, Aldo Merotto Junior, Ohn Mar Aung, Ramaiah Venuprasad, Ajay Kohli, Wenbin Zhou, Qian Qian
{"title":"Global wild rice germplasm resources conservation alliance: World Wild-Rice Wiring.","authors":"Xiaoming Zheng, Disna Ratnasekera, Jiayu Fan, Robert J Henry, Beng-Kah Song, Kenneth M Olsen, Bal Krishna Joshi, Maria Celeste N Banaticla-Hilario, Tonapha Pusadee, Adane Getachew Melaku, Yêyinou Laura Estelle Loko, Koukham Vilayheuang, Gavers K Oppong, Samuel Aduse Poku, Peterson W Wambugu, Song Ge, Aldo Merotto Junior, Ohn Mar Aung, Ramaiah Venuprasad, Ajay Kohli, Wenbin Zhou, Qian Qian","doi":"10.1016/j.molp.2024.03.001","DOIUrl":"10.1016/j.molp.2024.03.001","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039828","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
FERONIA-mediated TIR1/AFB2 oxidation stimulates auxin signalling in Arabidopsis. FERONIA 介导的 TIR1/AFB2 氧化可刺激拟南芥中的辅助素信号。
IF 27.5 1区 生物学
Molecular Plant Pub Date : 2024-04-01 DOI: 10.1016/j.molp.2024.04.002
Baiyan Lu, Shengnan Wang, Hanqian Feng, Jing Wang, Kaixing Zhang, Yilin Li, Ping Wu, Minmin Zhang, Yanshu Xia, Chao Peng, Chao Li
{"title":"FERONIA-mediated TIR1/AFB2 oxidation stimulates auxin signalling in Arabidopsis.","authors":"Baiyan Lu, Shengnan Wang, Hanqian Feng, Jing Wang, Kaixing Zhang, Yilin Li, Ping Wu, Minmin Zhang, Yanshu Xia, Chao Peng, Chao Li","doi":"10.1016/j.molp.2024.04.002","DOIUrl":"https://doi.org/10.1016/j.molp.2024.04.002","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":27.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140763409","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
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