Molecular Plant最新文献_第10页

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":"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.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"972-985"},"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":"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.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"725-746"},"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 4 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

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

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 4 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

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 4 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

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 4 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

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 17.1 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":"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 N6-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.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"531-551"},"PeriodicalIF":17.1,"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 17.1 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

引用次数: 0

Genomic selection in plant breeding: Key factors shaping two decades of progress. 植物育种中的基因组选择：影响二十年进展的关键因素。

IF 4 1区生物学

Molecular Plant Pub Date : 2024-04-01 Epub Date: 2024-03-12 DOI: 10.1016/j.molp.2024.03.007

Admas Alemu, Johanna Åstrand, Osval A Montesinos-López, Julio Isidro Y Sánchez, Javier Fernández-Gónzalez, Wuletaw Tadesse, Ramesh R Vetukuri, Anders S Carlsson, Alf Ceplitis, José Crossa, Rodomiro Ortiz, Aakash Chawade

{"title":"Genomic selection in plant breeding: Key factors shaping two decades of progress.","authors":"Admas Alemu, Johanna Åstrand, Osval A Montesinos-López, Julio Isidro Y Sánchez, Javier Fernández-Gónzalez, Wuletaw Tadesse, Ramesh R Vetukuri, Anders S Carlsson, Alf Ceplitis, José Crossa, Rodomiro Ortiz, Aakash Chawade","doi":"10.1016/j.molp.2024.03.007","DOIUrl":"10.1016/j.molp.2024.03.007","url":null,"abstract":"Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP-theoretically reaching one when using the Pearson's correlation as a metric-is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"552-578"},"PeriodicalIF":4.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140110790","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