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Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

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Journal of Integrative plant biology 2024年第2期66卷 228-251页

作者： Yezi Xiang Taikui Zhang Yiyong Zhao Hongjin Dong Hongyi Chen Yi Hu Chien-Hsun Huang Jun Xiang Hong Ma State key laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of biology Howard Hughes Medical InstituteDuke UniversityDurhamNC 27708USA Department of biology the Eberly College of Scienceand the Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA 16802USA Hubei key laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggang 438000China

Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and *** we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain *** this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial *** robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and ***,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple *** of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and *** new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversificat

关键词： angiosperm fruit evolution MADS-box molecular clock nuclear phylogeny ovary and fruit developmental genes

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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Molecular plant 2024年第2期17卷 240-257页

作者： Wei Li Jiaqi Liu Zeqi Li Ruiqiang Ye Wenzhen Chen Yuqing Huang Yue Yuan Yi Zhang Huayi Hu Peng Zheng Zhongming Fang Zeng Tao Shiyong Song Ronghui Pan Jian Zhang Jumim Tu Jen Sheen Hao Du State key laboratory of Rice biology College of Agriculture and BiotechnologyZhejiang UniversityYu-Hang-Tang Road No.866Hangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Hainan Institute of Zhejiang University Sanya 572025China National key laboratory of plant Molecular Genetics CASCenter for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChineseAcademy of SciencesShanghai 200032China key laboratory of plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Agricultural SciencesGuizhouUniversityGuiyang 550025China State key laboratory of Rice biology and Breeding China National Rice Research InstituteHangzhou 311400China Department of Molecular biology and Center for Computational and Integrative biology Massachusetts General Hospitaland Department of GeneticsHarvard Medical SchoolBostonMA02114USA

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy *** address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice ***,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under *** profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR ***,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under ***,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen *** further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated ***,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and *** study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

关键词： target of rapamycin TOR water-saving rice low-carbon agriculture drought nitrogen use efficiency NUE

Pan-genome analysis reveals a highly plastic genome and extensive secreted protein polymorphism in Puccinia striformis ***

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Journal of Genetics and Genomics 2024年第5期51卷 574-577页

作者： Jierong Wang Yuxi Peng Yiwen Xu Zhiru Li Gangming Zhan Zhensheng Kang Jing Zhao College of plant Protection Northwest A&F UniversityYanglingShaanxi 712100China State key laboratory of Crop stress biology for Arid Areas Northwest A&F UniversityYanglingShaanxi 712100China College of Life Science Northwest A&F UniversityYanglingShaanxi 712100China

The obligate biotrophic basidiomycete fungus Puccinia striformis ***(Pst)is the causative agent of wheat stripe(yellow)rust,a disease that results in severe damage to global wheat production(Chen and Kang,2017).This pathogen has a mixed reproductive mode encompassing both asexual and sexual *** asexual stage is accomplished by reinfecting wheat with urediniospores,while the sexual cycle involves five different spore types and two phylogenetically unrelated plant hosts wheat,which is the primary host,and barberry,which is the alternate host(Zhao et al.,2016).This extremely complex lifecycle facilitates large genetic variation among Pst populations,which is conducive to the emergence of new virulent races that can overcome wheat resistance genes,resulting in epidemics(Chen and Kang,2017).Secreted effector proteins,the key virulence factors in fungal pathogens,can not only suppress plant immune systems but also trigger host immune responses following recognition by plant receptors(Toruno et al.,2016).

关键词： Puccinia overcome wheat

Resistance development,cross-resistance,and fitness costs associated with Aphis gossypii resistance towards sulfoxaflor and acetamiprid in different geographical regions

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Journal of Integrative Agriculture 2024年第7期23卷 2332-2345页

作者： Wei Wang Renfu Zhang Haiyang Liu Ruifeng Ding Qiushi Huang Ju Yao Gemei Liang key laboratory of Integrated Pest Management on Crop in Northwestern Oasis of Ministry of Agriculture and Rural Affairs Institute of Plant ProtectionXinjiang Academy of Agricultural SciencesUrumqi 830091China State key laboratory for biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China

Aphis gossypii has become increasingly difficult to manage due to its strong insecticide *** the laboratory,we established sulfoxaflor-resistant and acetamiprid-resistant strains in two *** populations with different basal insecticide resistance levels,and evaluated the effects of basal insecticide resistance on the resistance development and cross-resistance,as well as differences in *** the same selection pressure,Yarkant ***(with low basal insecticide resistance)evolved resistance to sulfoxaflor and acetamiprid more quickly than Jinghe ***(with high basal insecticide resistance),and the evolution of *** resistance to sulfoxaflor developed faster than acetamiprid in both Yarkant and Jinghe,Xingjiang,*** sulfoxaflor-resistant strains selected from Yarkant and Jinghe developed significant cross-resistance to acetamiprid,imidacloprid,thiamethoxam and pymetrozine;while the acetamiprid-resistant strains developed significant cross-resistance to sulfoxaflor,imidacloprid,thiamethoxam,pymetrozine,and *** relative fitness of *** decreased as the resistance to sulfoxaflor and acetamiprid *** relative fitness levels of the sulfoxaflor-resistant strains(Yarkant-SulR and Jinghe-SulR)were lower than those of the acetamipridresistant strains(Yarkant-AceR and Jinghe-AceR).In addition,the relative fitness levels of sulfoxaflor-and acetamiprid-resistant strains were lower in Jinghe than in *** summary,basal insecticide resistance of *** and insecticide type affected the evolution of resistance to insecticides in ***,as well as cross-resistance to other *** sulfoxaflor-and acetamiprid-resistant *** strains had obvious fitness *** results of this work will contribute to the insecticide resistance management and integrated management of ***.

关键词： Aphis gossypii sulfoxaflor acetamiprid cross-resistance fitness costs different sensitivities

Seed Storability in Rice: Physiological Foundations, Molecular Mechanisms, and Applications in Breeding

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Rice science 2024年第4期31卷 401-416,I0023-I0024页

作者： ZHOU Tianshun YU Dong WU Liubing XU Yusheng DUAN Meijuan YUAN Dingyang Longping Branch College of BiologyHunan UniversityChangsha 410125China State key laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangsha 410125China Hunan Provincial key laboratory of Rice stress biology College of AgronomyHunan Agricultural UniversityChangsha 410128China

Long-term storage of crop seeds is critical for the conservation of germplasm resources, ensuring food supply, and supporting sustainable production. Rice, as a major food staple, has a substantial stock for consumption and production worldwide. However, its food value and seed viability tend to decline during storage. Understanding the physiological responses and molecular mechanisms of aging tolerance forms the basis for enhancing seed storability in rice. This review outlines the latest progress in influential factors, evaluation methods, and identification indices of seed storability. It also discusses the physiological consequences, molecular mechanisms, and strategies for breeding aging-tolerant rice in detail. Finally, it highlights challenges in seed storability research that require future attention. This review offers a theoretical foundation and research direction for uncovering the mechanisms behind seed storability and breeding aging-tolerant rice.

关键词： rice seed storability physiological response molecular mechanism aging-tolerant breeding

Single-cell transcriptomic landscape of peripheral blood cells provides insights into adaptation of red-eared sliders(Trachemys scripta elegans)

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Integrative Zoology 2024年第3期19卷 468-479页

作者： Rui GUO Guangwei MA Xiaofei ZHAI Haitao SHI Jichao WANG Ministry of Education key laboratory for Ecology of Tropical Islands Key Laboratory of Tropical Animal and Plant Ecology of Hainan ProvinceCollege of Life SciencesHainan Normal UniversityHaikouChina

Red-eared sliders(Trachemys scripta elegans),as one of the 100 most threatening aliens,have stronger immunity than the native species in response to environmental *** cells are an important component of immunity in the ***,the blood cell researches of turtle are still in the traditional blood cell classification and morphological structure ***,turtle granulocytes cannot be accurately identified using traditional ***-cell RNA sequencing techniques have been successfully implemented to study cells based on the mRNA expression patterns of each *** present study profiled the transcriptomes of peripheral blood cells in red-eared sliders to construct a single-cell transcriptional landscape of the different cell types and explored environmental adaptation mechanism from the perspective of *** 14 transcriptionally distinct clusters(platelets,erythrocytes1,erythrocytes2,CSF1R monocytes,POF1B monocytes,neutrophils,GATA2high basophils,GATA2low basophils,CD4 T cells,CD7 T cells,B cells,ACKR4 cells,serotriflin cells,and ficolin cells)were identified in the peripheral blood cells of the red-eared *** particular,a subtype of erythrocytes(erythrocytes1)that expressed immune signals was *** blood cells were grouped into three lineages:platelet,erythroid/lymphoid,and myeloid cell ***,based on differentiation trajectory and up-regulated gene expression,ACKR4 cells were newly identified as lymphocytes,and serotriflin and ficolin cells as *** single-cell transcriptional atlas of the peripheral blood cells in red-eared sliders provided in the present study will offer a comprehensive transcriptome reference for the exploration of physiological and pathological hematology in this species.

关键词： blood cells single-cell RNA-seq Trachemys scripta elegans

OsATL32 ubiquitinates the reactive oxygen species-producing OsRac5-OsRbohB module to suppress rice immunity

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Journal of Integrative plant biology 2024年第7期66卷 1459-1480页

作者： Yuqing Yan Hui Wang Yan Bi Jiajing Wang Muhammad Noman Dayong Li Fengming Song National key laboratory for Rice biology and Breeding Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Ministry of Agriculture key laboratory of Molecular biology of Crop Pathogens and Insect Pests Institute of BiotechnologyZhejiang UniversityHangzhou 310058China key laboratory of biology of Crop Pathogens and Insects of Zhejiang Province Institute of BiotechnologyZhejiang UniversityHangzhou 310058China

Ubiquitination-mediated protein degradation is integral to plant immunity,with E3 ubiquitin ligases acting as key factors in this ***,we report the functions of OsATL32,a plasma membrane-localized Arabidopsis Tóxicos En Levadura(ATL)-type E3 ubiquitin ligase,in rice(Oryza sativa)immunity and its associated regulatory *** found that the expression of OsATL32 is downregulated in both compatible and incompatible interactions between rice and the rice blast fungus Magnaporthe *** OsATL32 protein level declines in response to infection by a compatible *** strain or to chitin ***32 negatively regulates rice resistance to blast and bacterial leaf blight diseases,as well as chitin-triggered *** and genetic studies revealed that OsATL32 suppresses pathogen-induced reactive oxygen species(ROS)accumulation by mediating ubiquitination and degradation of the ROS-producing OsRac5–OsRbohB module,which enhances rice immunity against *** protein phosphatase PHOSPHATASE AND TENSIN HOMOLOG enhances rice blast resistance by dephosphorylating OsATL32 and promoting its degradation,preventing its negative effect on rice *** study provides insights into the molecular mechanism by which the E3 ligase OsATL32 targets a ROS-producing module to undermine rice immunity.

关键词： E3 ligase OsATL32 OsRac5-OsRbohB module phosphatase OsPTEN reactive oxygen species rice immunity

Rice gene OsUGT75A regulates seedling emergence under deep-sowing conditions

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The Crop Journal 2024年第1期12卷 133-141页

作者： Jia Zhao Siyu Liu Xiaoqian Zhao Zhibo Huang Shan Sun Zixuan Zeng Yongqi He Zhoufei Wang The laboratory of Seed Science and Technology Guangdong Key Laboratory of Plant Molecular BreedingNational Engineering Research Center of Plant Space BreedingSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field *** we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot *** of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing *** of free abscisic acid(ABA)and jasmonates(JA)were higher in shoots of OsUGT75A mutants than in those of wild-type plants,and OsUGT75A mutants were more sensitive to ABA and JA *** shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in *** extension by OsUGT75A is achieved mainly by promotion of cell *** elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice ***75A acts to increase seedling emergence under deep-sowing conditions.

关键词： Abscisic acid Deep-sowing Jasmonic acid Rice Shoot length

Perenniality:From model plants to applications in agriculture

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Molecular plant 2024年第1期17卷 141-157页

作者： Bo Zhao Jia-Wei Wang National key laboratory of plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences(CEMPS)Institute of Plant Physiology and Ecology(SIPPE)Chinese Academy of Sciences(CAS)Shanghai 200032China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China key laboratory of plant Carbon Capture CASShanghai 200032China New Cornerstone Science laboratory Shanghai 200032China

To compensate for their sessile nature,plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing *** such prominent feature is the evolution of diverse life history strategies,particularly such that annuals reproduce once followed by seasonal death,while perennials live longer by cycling growth *** intrinsic phenology is primarily genetic and can be altered by environmental *** evolutionary transitions between annual and perennial life history strategies are common,perennials account for most species in nature because they survive well under year-round *** proportion,however,is reversed in ***,perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate *** significant endeavors that have been made to generate perennial crops,progress is slow because of barriers in studying perennials,and many developed species await further *** findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle *** implies that engineering plant life history strategy can be achieved by manipulating only a few key *** this review,we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.

关键词： perenniality developmental plasticity flowering time poplar Arabis alpina perennial crops life history strategy