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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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Molecular plant 2024年第5期17卷 725-746页

作者： 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 Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea plant Science Centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean Centre for plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** 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 *** 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 *** comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).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.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution

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RebL1 is required for macronuclear structure stability and gametogenesis in Tetrahymena thermophila

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Marine Life Science & Technology 2024年第2期6卷 183-197页

作者： Huijuan Hao Yinjie Lian Chenhui Ren Sitong Yang Min Zhao Tao Bo Jing Xu Wei Wang Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education Institute of BiotechnologyShanxi UniversityTaiyuan 030006China School of Life Science Shanxi UniversityTaiyuan 030006China Shanxi Key Laboratory of biotechnology Taiyuan 030006China

Histone modification and nucleosome assembly play important roles in chromatin-related *** chaperones form different complexes and coordinate histone transportation and *** histone chaperone complexes have been identified in different *** ciliate protozoa(ciliates)have various chromatin structures and different nuclear ***,histone chaperone components and functions of different subunits remain unclear in ***-rahymema thermophila contains a transcriptionally active macronucleus(MAC)and a transcriptionally inactive micronu-cleus(MIC)which exhibit multiple replication and various chromatin remodeling progresses during vegetative growth and sexual developmental ***,we found histone chaperone RebL1 not only localized evenly in the transcriptionally active MAC but also dynamically changed in the MIC during vegetative growth and sexual developmental ***1 knockdown inhibited cellular *** macronuclear morphology became bigger in growing *** abnormal macronuclear structure also occurred in the starvation ***,micronuclear meiosis was disturbed during sexual development,leading to a failure to generate new gametic ***1 potentially interacted with various factors involved in histone-modifying complexes and chromatin remodeling complexes in different developmental ***1 knockdown affected expression levels of the genes involved in chromatin organization and *** together,RebL1 plays a vital role in maintaining macronuclear structure stability and gametogenesis in ***.

关键词： Gametogenesis Histone chaperone Macronuclear structure RebL1 Tetrahymena thermophilaIntroduction

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BFP1:One of 700 Arabidopsis F-box proteins mediates degradation of JA oxidases to promote plant immunity

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Molecular plant 2024年第3期17卷 375-376页

作者： Claus Wasternack Bettina Hause Department of Molecular Signal Processing Leibniz Institute of Plant Biochemistry7 Weinberg 306120 Halle(Saale)Germany Department of Cell and Metabolic Biology Leibniz Institute of Plant Biochemistry06120 Halle(Saale)Germany

A switch off in jasmonate(JA)signaling by hydroxylation upon wounding was described in 2008(Miersch et al.,2008).This initiated the cloning of CYP450 enzymes involved in hydroxylation and carboxylation of JA and its amino acid conjugate JA-le,the most active form of JA compounds(reviewed by Wasternack and Feussner[2018]and Heitz et al.[2019]).Due to the central role of JA and JA-lle in plant stress responses and development(Wasternack and Hause,2013),catabolism of JA and its derivatives is an essential component in the sustainment of homeostasis of active JA compounds(Howe et al.,2018;Heitz et al.,2019).Catabolism of JA and JAIle takes place by JA-induced oxygenases(JOXs),also named JA-oxidases(JAOs),and by hydroxylation(CYP94B3/B1)followed by carboxylation(CYP94C1),respectively(Heitz et al.,2019).Another reaction performed by IAR3/ILL6 results in the deconjugation of JA-lle and 12-OH-JA-le to JA and 12-OH-JA,respectively(Heitz et al.,2019;Wasternack and Feussner,2018).

关键词： conjugate initiated media

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Microbe-induced gene silencing explores interspecies RNAi and opens up possibilities of crop protection

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Science China(Life Sciences) 2024年第3期67卷 626-628页

作者： Rongxiang Fang State Key Laboratory of plant Genomics Institute of MicrobiologyChinese Academy of Sciencesand National Plant Gene Research CenterBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

In most eukaryotes, small RNA(sRNA)-mediated RNA silencing(or RNA interference, RNAi) is an evolutionarily conserved mechanism that regulates gene expression in a sequence-specific ***, s RNAs are produced by the RNase III enzymes Dicers and then incorporated into Argonaute(AGO) proteins to regulate gene expression by mRNA degradation.

关键词： protection conserved manner

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Carbonic anhydrase-like enzymes in the formation of Lycopodium alkaloid

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Chinese Journal of Natural Medicines 2024年第3期22卷 193-194页

作者： DONG Huiwen GE Huiming State key Laboratory of Pharmaceutical biotechnology Institute of Functional BiomoleculesSchool of Life SciencesNanjing UniversityNanjing 210023China

plant alkaloids,renowned for their structural diversity and bioactivity,are prominent in both modern and traditional medicine[1].Unraveling the intricacies of plant alkaloid biosynthesis could pave the way for the discovery of new natural products and *** may also shed light on the roles of existing pathways in host biology and provide valuable tools for metabolic engineering in plants and microbes[2].Unlike other major classes of plant natural products,such as terpenoids and polyketides,the formation of alkaloid scaffolds does not conform to a uniform chemical theme or depend on a singular enzyme class[3].A case in point is the Lycopodium alkaloids in the Lycopodiaceae family,where the enzymes responsible for their core scaffold construction remain unidentified[4].

关键词： Lycopodium alkaloid Carbonic anhydrase-like enzymes Biosynthesis

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RACK1A promotes hypocotyl elongation by scaffolding light signaling components in Arabidopsis

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Journal of Integrative plant Biology 2024年第5期66卷 956-972页

作者： Yajuan Fu Wei Zhu Yeling Zhou Yujing Su Zhiyong Li Dayan Zhang Dong Zhang Jinyu Shen Jiansheng Liang Key Laboratory of Molecular Design for plant Cell Factory of Guangdong Higher Education institutes Department of BiologySchool of Life SciencesInstitute of Plant and Food SciencesSouthern University of Science and TechnologyShenzhen 518055China

plants deploy versatile scaffold proteins to intricately modulate complex cell *** these,RACK1A(Receptors for Activated C Kinase 1A)stands out as a multifaceted scaffold protein functioning as a central integrative hub for diverse signaling ***,the precise mechanisms by which RACK1A orchestrates signal transduction to optimize seedling development remain largely ***,we demonstrate that RACK1A facilitates hypocotyl elongation by functioning as a flexible platform that connects multiple key components of light signaling ***1A interacts with PHYTOCHROME INTERACTING FACTOR(PIF)3,enhances PIF3 binding to the promoter of BBX11 and down-regulates its ***,RACK1A associates with ELONGATED HYPOCOTYL 5(HY5)to repress HY5 biochemical activity toward target genes,ultimately contributing to hypocotyl *** darkness,RACK1A is targeted by CONSTITUTIVELY PHOTOMORPHOGENIC(COP)1 upon phosphorylation and subjected to COP1-mediated degradation via the 26 S proteasome *** findings provide new insights into how plants utilize scaffold proteins to regulate hypocotyl elongation,ensuring proper skoto-and photo-morphogenic development.

关键词： Arabidopsis hypocotyl development light signaling components RACK1 scaffoldprotein

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Patterns and drivers of plant sexual systems in the dry-hot valley region of southwestern China

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plant Diversity 2024年第2期46卷 158-168页

作者： Rong Ma Qi Xu Yongqian Gao Deli Peng Hang Sun Bo Song State Key Laboratory of plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of plant Species with Extremely Small Populations Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China College of Life Sciences Shaanxi Normal UniversityXi'an 710119China Yunnan Forestry Technological College Kunming 650224China School of Life Science/Key Laboratory of Yunnan for Biomass Energy and biotechnology of Environment Yunnan Normal UniversityKunming 650500YunnanChina

Sexual systems play important roles in angiosperm evolution and exhibit substantial variations among different floras. Thus, studying their evolution in a whole flora is crucial for understanding the formation and maintenance of plant biodiversity and predicting its responses to environmental change. In this study, we determined the patterns of plant sexual systems and their associations with geographic elements and various life-history traits in dry-hot valley region of southwestern China, an extremely vulnerable ecosystem. Of the 3166 angiosperm species recorded in this area, 74.5% were hermaphroditic,13.5% were monoecious and 12% were dioecious, showing a high incidence of diclinous species. Diclinous species were strongly associated with tropical elements, whereas hermaphroditic species were strongly associated with temperate and cosmopolitan elements. We also found that hermaphroditism was strongly associated with showy floral displays, specialist entomophily, dry fruits and herbaceous *** was strongly associated with inconspicuous, pale-colored flowers, generalist entomophily, fleshy fruits, and woody plants, whereas monoecy was strongly associated with inconspicuous, pale-colored flowers, anemophily, dry fruits, and herbaceous plants. In addition, hermaphroditic species with generalist entomophily tended to flower in the dry season, whereas diclinous species with specialist entomophily tended to flower in the rainy season. However, independent of sexual systems, plants that produce dry fruits tended to flower in the rainy season and set fruits in the dry season, but the opposite pattern was found for fleshy fruit-producing plants. Our results suggest that in the dry-hot valleys, plant sexual systems are associated with geographic elements as well as various life-history traits that are sensitive to environmental change.

关键词： Floral traits Fruit type Growth form Pollination system Reproductive phenology

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Knock-out of BnHva22c reduces the susceptibility of Brassica napus to infection with the fungal pathogen Verticillium longisporum

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The Crop Journal 2024年第2期12卷 503-514页

作者： Wanzhi Ye Roxana Hossain Michael Prbsting Abdallah Abdelmegid Mohamed Ali Lingyue Han Ying Miao Steffen Rietz Daguang Cai Dirk Schenke Department of Molecular Phytopathology and biotechnology Institute of PhytopathologyChristian-Albrechts-University of KielKielGermany Institut für Zuckerrübenforschung GöttingenGermany plant Pathology Department Faculty of Agriculture and Natural ResourcesAswan UniversityAswanEgypt Fujian Provincial Key Laboratory of plant Functional Biology College of Life SciencesFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Hohenlieth-Hof NPZ Innovation GmbHHoltseeGermany

Verticillium longisporum(Vl43)is a soilborne hemibiotrophic fungal pathogen causing stem striping on oilseed rape(OSR)and severe yield *** for resistant varieties is the most promising approach to control this ***,we report the identification of Hva22c as a novel susceptibility factor and its potential for improving OSR ***22c is a member of the Hva22 gene family,originally described for barley(Hordeum vulgare).Several Hva22 members have been located at the endoplasmic ***22c is up-regulated in response to Vl43 in both Arabidopsis and *** demonstrate that knock-out of Hva22c in OSR by CRISPR/Cas9 and its homolog in Arabidopsis by T-DNA insertion reduced plants’susceptibility to Vl43 infection and impaired the development of disease *** understand the underlying mechanism,we analysed transcriptomic data from infected and non-infected roots of hva22c knock-out and wild type *** identified a homozygous mutant with frame-shifts in all four BnHva22c loci displaying a vastly altered transcriptional landscape at 6 ***,a large set of genes was suppressed under mock conditions including genes related to the endomembrane *** the up-regulated genes we found several defense-related and phytohormone-responsive genes when comparing mutant to the wild *** results demonstrate that Hva22c is functionally required for a fully compatible plant-fungus *** loss of function reduces plant susceptibility,most likely due to endoplasmatic reticulum and Golgi dysfunction accompanied by additionally activated defense *** findings can help improve OSR resistance to *** infection.

关键词： Hva22c Susceptibility factor CRISPR/Cas9 Brassica napus Arabidopsis Verticillium longisporum Resistance breeding

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A numerical and experimental comparison of heat transfer in a quasi two-dimensional packed bed

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Particuology 2024年第1期84卷 136-144页

作者： Matthias Tyslik Mirko Ebert Martin Schiemann Siegmar Wirtz Christian Lessig Department of Energy plant Technology Ruhr-University BochumGermany institute for Simulation and Graphics Otto-von-Guericke-Universität MagdeburgGermany

Heat transfer plays a major role in many industrial processes taking place in packed *** accurate and reliable simulation of the heat exchange between particles is therefore crucial for a reliable operation and to optimize the processes in the *** discrete ordinates method(DOM)provides an established numerical technique to model radiative heat transfer in granular media that offers the possibility to consider the directional dependence of the radiation *** this work,DOM is compared with Monte Carlo ray tracing,which provides an alternative method for heat transfer ***-rically simple configurations are used to investigate the influence of the angular discretization on the accuracy of the results and the computation time in both *** obtained insights are then transferred to a more complex configuration of a quasi two-dimensional test rig consisting of metal rods for which also experimental results are *** results show that both DOM and Monte Carlo ray tracing allow for an accurate simulation of heat transfer in packed *** Carlo ray tracing requires thereby computation times that are surprisingly competitive(although still somewhat slower)compared to DOM and allows for an easier computation of highly accurate reference *** our preliminary comparison to the experimental test rig,Monte Carlo ray tracing also provides the advantage that it can more easily model highly specular materials such as stainless *** methods are comparable for diffuse materials such as magnesium oxide.

关键词： Heat transfer Discrete ordinates method Monte Carlo ray tracing

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Regulation of gene-edited plants in Europe:from the valley of tears into the shining sun?

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aBIOTECH 2024年第2期5卷 231-238页

作者： Holger Puchta Department of Molecular Biology Joseph Gottlieb Kolreuter Institute for Plant SciencesKarlsruhe Institute of Technology(KIT)Fritz-Haber-Weg 476131 KarlsruheGermany

Some 20 years ago,the EU introduced complex regulatory rules for the growth of transgenic crops,which resulted in a de facto ban to grow these plants in fields within most European *** the rise of novel genome editing technologies,it has become possible to improve crops genetically in a directed way without the need for incorporation of foreign ***,in 2018,the European Court of Justice ruled that such gene-edited plants are to be regulated like transgenic *** then,European scientists and breeders have challenged this decision and requested a revision of this outdated ***,after 5 years,the European Commission has now published a proposal on how,in the future,to regulate crops produced by new breeding *** proposal tries to find a balance between the different interest groups in *** one side,genetically modified plants,which cannot be discerned from their natural counterparts,will exclusively be used for food and feed and are-besides a registration step-not to be regulated at *** the other side,plants expressing herbicide resistance are to be excluded from this regulation,a concession to the strong environmental associations and NGOs in ***,edited crops are to be excluded from organic farming to protect the business interests of the strong organic sector in ***,if this law passes European parliament and council,unchanged,it will present a big step forward toward establishing a more sustainable European agricultural ***,it might soon be possible to develop and grow crops that are more adapted to global warming and whose cultivation will require lower amounts of ***,there is still a long way to go until the law is *** often,the storm of arguments raised by the opponents,based on irrational fears of mutations and a naive understanding of nature,has fallen on fruitful ground in Europe.

关键词： Genetically modified organism Cisgenesis Gene editing CRISPR/Cas Regulation

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