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SapBase:A central portal for functional and comparative genomics of Sapindaceae species

Journal of Integrative plant biology 2024年第8期66卷 1561-1570页

作者： Jiawei Li Chengjie Chen Zaohai Zeng Fengqi Wu Junting Feng Bo Liu Yingxiao Mai Xinyi Chu Wanchun Wei Xin Li Yanyang Liang YuanLong Liu Jing Xu Rui Xia State key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhou 510640China Guangdong laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhou 510640China key laboratory of biology and germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs South China Agricultural UniversityCollege of HorticultureGuangzhou 510640China

The Sapindaceae family,encompassing a wide range of plant forms such as herbs,vines,shrubs,and trees,is widely distributed across tropical and subtropical *** family includes economically important crops like litchi,longan,rambutan,and *** the wide application of genomic technologies in recent years,several Sapindaceae plant genomes have been decoded,leading to an accumulation of substantial omics data in this *** surge in data highlights the pressing need for a unified genomic data center capable of storing,sharing,and analyzing these ***,we introduced SapBase,that is,the Sapindaceae Genome *** houses seven published plant genomes alongside their corresponding gene structure and functional annotations,small RNA annotations,gene expression profiles,gene pathways,and synteny block *** offers user-friendly features for gene information mining,co-expression analysis,and interspecies comparative genomic ***,we showcased SapBase's extensive capacities through a detailed bioinformatic analysis of a MYB gene in ***,Sap Base could serve as an integrative genomic resource and analysis platform for the scientific exploration of Sapinaceae species and their comparative studies with other plants.

关键词： functional crops unified

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Functional Characterization of a Novel Chloroplast-targeting Non-classically Secreted Protein(PcCt2) in the Pathogenesis of Phytophthora capsici

Functional Characterization of a Novel Chloroplast-targeting...

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中国植物病理学会2024年学术年会

作者： HUA Cai LAI Bingting QIU Xiang GUO Yaru XU Kaiyi LI Linying ZHANG Kaidi GUO Hengyuan LIU Wenbo Justice Norvienyeku key laboratory of Green Prevention and Control of tropical plant Diseases and Pests Ministry of EducationSchool of Tropical Agriculture and ForestryHainan University Danzhou Invasive Species Observation and Research Station of hainan Province Hainan University

The oomycetes Phytophthora capsici is an economically destructive plant pathogen that causes Phytophthora-blight disease in multiple fruit and vegetable crops,including Capsicum annum,Solanum lycopersicum,Citrullus lanatus,Vicia faba,Solanum melongena among *** Phytophthora-blight pathogen remains a significant threat to global food security due to inadequate knowledge of the molecular determinants of pathogenicity or virulence of *** during pathogen-host interaction to support the development of sustainable and environmentally friendly disease control *** and effectome analysis revealed a hypothetical protein containing chloroplast-targeting peptide(cTP) in ***(PcCt2) as a novel non-classically secreted candidate effector protein that targets host chloroplast during pathogen-host ***,we deployed transcriptomic,biochemical,and functional geneticstrategies,including CRISPR-Cas9 gene editing and homologous recombination approach to generate PcCT2 targeted gene replacement *** exclusive and significant up-regulation in the expression pattern of PcCT2 at early and late stages of *** interaction with pepper,tomato,faba bean,kidney bean,watermelon,and *** the same time,phenotypic characterization of the ΔPcct2 strains showed that targeted replacement of PcCT2 triggered a significant reduction in the vegetative growth,sporulation,stress tolerance,and virulence of ***-fold2-based pairwise screening of pepper proteome with PcCT2 identified 16 chloroplast localized putative interaction *** from Yeast-two-hybrid analysis confirmed a physical-geneticinteraction between PcCT2 and chloroplast localized Ethylene-responsive transcription *** findings underscore the significance of non-classically secreted effector proteins in the pathogenesis of *** and also projected PcCT2 as a potential target for developing oomyticides against the Phytophthora-blight pa

关键词： Phytophthora capsici effector protein Pathogen-host interaction Microbial Pathogenesis Non-classically secreted protein

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Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations

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Journal of Integrative plant biology 2024年第7期66卷 1385-1407页

作者： Lirong Zhao Yunwei Liu Yi Zhu Shidie Chen Yang Du Luyao Deng Lei Liu Xia Li Wanqin Chen Zhiyu Xu Yangyang Xiong You Ming Siyu Fang Ligang Chen Houping Wang Diqiu Yu CAS key laboratory of tropical plant Resources and Sustainable Use Xishuangbanna Tropical Botanical GardenThe Chinese Academy of SciencesMengla 666303China College of Life Sciences University of Chinese Academy of SciencesBeijing 101408China State key laboratory for Conservation and Utilization of Bio‐resources in Yunnan Yunnan UniversityKunming 650500China School of Life Sciences Yunnan UniversityKunming 650500China Southwest United Graduate School Yunnan UniversityKunming 650092China

The heading date of rice is a crucial agronomic characteristic that influences its adaptability to different regions and its productivity *** the involvement of WRKY transcription factors in various biological processes related to development,the precise mechanisms through which these transcription factors regulate the heading date in rice have not been well *** present study identified OsWRKY11 as a WRKY transcription factor which exhibits a pivotal function in the regulation of the heading date in rice through a comprehensive screening of a clustered regularly interspaced palindromic repeats(CRISPR)-CRISPR-associated nuclease 9 mutant library that specifically targets the WRKY genes in *** heading date of oswrky11 mutant plants and OsWRKY11-overexpressing plants was delayed compared with that of the wild-type plants under short-day and long-day *** investigation revealed that OsWRKY11 exerts dual effects on transcriptional promotion and suppression through direct and indirect DNA binding,*** normal conditions,OsWRKY11 facilitates flowering by directly inducing the expression of OsMADS14 and *** presence of elevated levels of OsWRKY11 protein promote formation of a ternary protein complex involving OsWRKY11,Heading date 1(Hd1),and Days to heading date 8(DTH8),and this complex then suppresses the expression of Ehd1,which leads to a delay in the heading *** investigation revealed that a mild drought condition resulted in a modest increase in OsWRKY11 expression,promoting ***,under severe drought conditions,a significant upregulation of OsWRKY11 led to the suppression of Ehd1 expression,ultimately causing a delay in heading *** findings uncover a previously unacknowledged mechanism through which the transcription factor OsWRKY11 exerts a dual impact on the heading date by directly and indirectly binding to the promoters of target genes.

关键词： heading date OsWRKY11 rice transcription factors

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Seedling dynamics differ between canopy species and understory species in a tropical seasonal rainforest,SW China

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plant Diversity 2024年第5期46卷 671-677页

作者： Libing Pan Xiaoyang Song Wenfu Zhang Jie Yang Min Cao CAS key laboratory of tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunMengla 666303YunnanChina College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

We used 11 years of census data from 450 seedling quadrats established in a 20-ha forest dynamics plot to study seedling dynamics in tree species of a tropical seasonal rainforest in Xishuangbanna,southwestern *** found that overall seedling recruitment rate and relative growth rate were higher in the rainy season than in the dry *** the recruitment rate of seedlings from canopy tree species(two species)and the relative growth rate of seedlings from understory species(nine species)were higher in the rainy season than in the dry ***,in the rainy season,the recruitment rate of seedlings was higher for canopy tree species than for understory tree *** addition,relative growth rate of seedlings was higher in the canopy species than in understory seedlings in the dry *** also observed that,in both rainy and dry seasons,mortality rate of seedlings was higher for canopy species than for understory ***,canopy tree species appear to have evolved a flexible strategy to adapt to the seasonal changes of a monsoon *** contrast,understory tree species seem to have adopted a conservative ***,these species mainly release seedlings in the rainy season and maintain relatively stable populations with a lower mortality rate and recruitment rate in both dry and rainy *** study suggests that canopy and understory seedling populations growing in forest understory may respond to future climate change scenarios with distinct regeneration strategies.

关键词： tropical forest Tree seedling Seasonality Recruitment Mortality Relative growth rate

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Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants

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Marine Life Science & Technology 2024年第3期6卷 425-441页

作者： Weicai Song Wenbo Shi Huan Wang Zirui Zhang Ruiqing Tao Jin Liu Shuo Wang Michael S.Engel Chao Shi College of Marine Science and Biological Engineering Qingdao University of Science and TechnologyQingdao 266042China plant germplasm and Genomics Center Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyThe Chinese Academy of SciencesKunming 650204China Yunnan Institute of tropical Crops Xishuangbanna 666100China American Museum of Natural History New YorkNY 10024-5192USA Natural History Museum and Department of Ecology&Evolutionary BiologyUniversity of KansasLawrenceKS 66045USA

The aquatic plant Nymphaea,a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae,has been extensively ***,the availability of chloroplast genome data for this genus is incomplete,and phylogenetic relationships within the order Nymphaeales remain *** this study,12 chloroplast genomes of Nymphaea were assembled and analyzed for the first *** genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes,including 79 protein-coding genes,30 tRNA genes,and four rRNA *** also report on codon usage,RNA editing sites,microsatellite structures,and new repetitive sequences in this *** genomics revealed that expansion and contraction of IR regions can lead to changes in the gene ***,it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic ***,the phylogenetic tree showed the order Nymphaeales was divided into three families,and the genus Nymphaea can be divided into five(or three)subgenera,with the subgenus Nymphaea being the *** divergence times of nymphaealean taxa were analyzed,with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years,*** results of the phylo-genetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.

关键词： Aquatic plants Nymphaea Phylogenetic analysis Plastid genomics Structural variation

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Transcriptome and metabolome analysis of preharvest internal browning in Nane plum fruit caused by high temperature

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Horticultural plant Journal 2024年第5期10卷 1099-1111页

作者： Cheng Peng Linping Deng Hejun Tan Wancong Meng Jianliang Luo Zengwen Zhang Huiqiong Chen Jishui Qiu Xiaoxiao Chang Yusheng Lu Institute of Fruit Tree Research Guangdong Academy of Agricultural SciencesKey Laboratory of South Subtropical Fruit Biology and Genetic Resource UtilizationMinistry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree ResearchGuangzhouGuangdong 510640China Lechang Lingnan Institute of Deciduous Fruit Tree Research ShaoguanGuangdong 512200China

The preharvest internal browning of Nane plum fruit,with no visible effects on the appearance of the fruit,has become a serious problem in recent years in its production area in Guangdong Province,*** study investigated the effects of environmental factors,including temperature,on Nane plum internal *** orchards at different elevations with different incidences of internal browning were *** fruits with different internal browning incidence levels,the internal browning mechanism was analyzed with transcriptome and metabolome *** results revealed decreased internal browning at high *** treatment significantly reduced internal browning,whereas bagging and insect-proof net-covering treatments significantly increased internal *** bagging and net coverings increase the local ambient temperature,the findings suggest that high temperature is an important factor influencing the internal browning of Nane *** metabolome experiments showed that with increased internal browning,the levels of phenolic hydroxyls such as catechol increased,with simultaneous increases in hydrogen peroxide content and oxidase *** can be speculated that the oxidation of phenolic hydroxyl substances is the main cause of the preharvest browning of Nane *** analysis revealed the increased expression of calcium signaling-related and downstream effector genes and indicated an important role of calcium in internal browning,possibly due to its increased content in the ***,with increasingly serious internal browning,genes related to photosynthesis were down-regulated,while genes related to senescence were up-regulated,thus suggesting the up-regulation of the process of cell senescence during internal *** conclusion,heat stress should be eliminated to reduce preharvest internal browning in Nane plum.

关键词： Nane plum Fruit internal browning High temperature Calcium

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FKF1b controls reproductive transition associated with adaptation to geographical distribution in maize

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Journal of Integrative plant biology 2024年第5期66卷 943-955页

作者： Suhui Chen Shan Gao Dongyang Wang Jie Liu Yingying Ren Zhihan Wang Xin Wei Qin Wang Xuehui Huang Shanghai key laboratory of plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China

Maize(Zea mays subspecies mays)is an important commercial crop across the world,and its flowering time is closely related to grain yield,plant cycle and latitude ***1 is an essential clock-regulated blue-light receptor with distinct functions on flowering time in plants,and its function in maize remains *** this study,we identified two FKF1 homologs in the maize genome,named ZmFKF1a and ZmFKF1b,and indicated that ZmFKF1a and ZmFKF1b independently regulate reproductive transition through interacting with ZmCONZ1 and ZmGI1 to increase the transcription levels of ZmCONZ1 and *** demonstrated that ZmFKF1b underwent artificial selection during modern breeding in China probably due to its role in geographical ***,our data suggested that ZmFKF1bHap_C7 may be an elite allele,which increases the abundance of ZmCONZ1 mRNA more efficiently and adapt to a wider range of temperature zone than that of ZmFKF1bHap_Z58 to promote maize floral *** extends our understanding of the genetic diversity of maize *** allele is expected to be introduced into tropical maize germplasm to enrich breeding resources and may improve the adaptability of maize at different climate zones,especially at temperate region.

关键词： flowering geographical distribution maize ZmFKF1

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Genetic diversity of RNA viruses infecting invertebrate pests of rice

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Science China(Life Sciences) 2024年第1期67卷 175-187页

作者： Haoran Wang Shufen Chao Qing Yan Shu Zhang Guoqing Chen Chonghui Mao Yang Hu Fengquan Yu Shuo Wang Liang Lv Baojun Yang Jiachun He Songbai Zhang Liangsheng Zhang Peter Simmonds Guozhong Feng State key laboratory of Rice biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311400China State key laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Institute of plant Protection&Soil Fertilizer Hubei Academy of Agricultural SciencesWuhan 430064China Institute of plant Protection Guizhou Academy of Agricultural SciencesGuiyang 550000China Institute of plant Protection Liaoning Academy of Agricultural SciencesShenyang 110161China Sanya Agricultural Technology Extension and Service Centre Sanya 572000China College of Agriculture Yangtze UniversityJingzhou 434000China Fujian Provincial key laboratory of Haixia Applied plant Systems biology Fujian Agriculture and Forestry UniversityFuzhou 350002China Genomics and Genetic Engineering laboratory of ornamental plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310012China Nuffield Department of Medicine Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxford OX13SYUnited Kingdom

Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop ***,information on viruses infecting invertebrate pests of crops is *** this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice *** identified 296 new RNA viruses and 13 known RNA *** viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and *** the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of *** detected known rice viruses in novel invertebrate hosts at high ***,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus *** potential insect pathogenic RNA viruses were detected in invertebrate *** analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral ***-species transmission of RNA viruses was detected between invertebrate *** identified viral genomes showed extensive variation for invertebrate viral families or ***,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

关键词： invertebrate species metatranscriptome viral diversity viral transmission viral genomes

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Vegetation changes across the Eocene-Oligocene transition:Global signals *** development

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Science China Earth Sciences 2024年第9期67卷 2937-2952页

作者： Mengxiao WU Lutz KUNZMANN Shufeng LI Vasilis TEODORIDIS Zhekun ZHOU Tao SU CAS key laboratory of tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla 666303China Senckenberg Natural History Collections Dresden Konigsbrücker LandstraBe 159Dresden 01109Germany Department of biology and Environmental Studies Faculty of EducationCharles UniversityMagdalény Rettigové411639 Prague 1Czech Republic State key laboratory of Oil and Gas Reservoir Geology and Exploitation Chengdu University of TechnologyChengdu 610059China Institute of Sedimentary Geology Chengdu University of TechnologyChengdu 610059China

The Eocene-Oligocene transition(EOT)marked a rapid global cooling event,often considered as the beginning of the modern icehouse *** by various factors,including tectonic activity and paleogeographic settings,the terrestrial records indicate a diverse response of fauna and vegetation to this global *** examined nine macrofossil assemblages from seven fossil localities on the southeastern margin of the Tibetan Plateau and from the mid-latitudinal Europe ranging from the latest Bartonian and Priabonian(37.71-33.9 Ma)to the Rupelian(33.9-27.82 Ma).Our aims were to trace and compare the vegetation history of both regions in the late Eocene and early *** results show that both regions experienced changes in vegetation composition in response to climate change,characterized by a decrease in the percentages of broad-leaved evergreen elements and distinctive changes in general vegetation types.A general change in the overall vegetation type from subtropical broad-leaved evergreen forests in the late Eocene to temperate broad-leaved mixed deciduous evergreen forests,or mixed mesophytic forests,in the early Oligocene is recognized in both *** results indicate a clear change in leaf architecture,leaf margin states,and secondary venation types in the mid-latitudinal Europe,while the results from the southeastern margin of the Tibetan Plateau show a distinct reduction in leaf *** data suggest that both global and regional factors played key roles in shaping the vegetation in the two regions.

关键词： Eocene-Oligocene transition plant fossil Paleoclimate Leaf architecture Biodiversity

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A commentary of“Mechanism of alkaline tolerance and application in crop improvement”:Top 10 Chinese Scientific Advances of 2023,China

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Fundamental Research 2024年第3期4卷 697-698页

作者： Yujuan Zhu Sanwen Huang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China State key laboratory of tropical Crop Breeding Chinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China

As global warming accelerates,soil degradation,exacerbated by extreme weather,has become a significant environmental issue ***,in particular,is grappling with a yearly reduction in arable land due to soil degradation,acidification,and salinization,posing potential threats to food *** country has a vast area of saline-alkaline land,over half of which are high-pH soda saline *** lands often experience simultaneous salt and alkali stress,severely inhibiting plant growth and crop ***,finding ways to utilize this marginal and saline-alkaline land for food production is a critical scientific *** this context,Chinese scientists have achieved a breakthrough towards harnessing saline-alkaline land.

关键词： alkaline utilize breakthrough

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