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Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

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Journal of Integrative Plant Biology 2024年第7期66卷 1408-1426页

作者： Tianhao Zhang Wenjing Peng Hua Xiao Shuo Cao Zhuyifu Chen Xiangnian Su Yuanyuan Luo Zhongjie Liu Yanling Peng Xiping Yang Guo-Feng Jiang Xiaodong Xu Zhiyao Ma Yongfeng Zhou National key laboratory of tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China State key laboratory for conservation and Utilization of subtropical Agro‐Bioresources Guangxi UniversityNanning 530004China Guangxi key laboratory of Forest Ecology and conservation Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest PlantationCollege of ForestryGuangxi UniversityNanning 530004China College of Informatics Huazhong Agricultural UniversityWuhan 430070China Guangxi key laboratory of Sugarcane Biology College of AgricultureGuangxi UniversityNanning 530004China key laboratory of Horticultural Plant Biology Ministry of Education Huazhong Agricultural UniversityWuhan 430070China Zhengzhou Fruit Research Institute Chinese Academy of Agricultural SciencesZhengzhou 450009China National key laboratory of tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 571101China

Structural variations(SVs)are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic *** this study,we employed woolly grape(Vitis retordii),a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats,as a valuable model for examining the impact of SVs on local *** assembled a haplotype-resolved chromosomal reference genome for woolly grape,and conducted population genetic analyses based on whole-genome sequencing(WGS)data from coastal and inland *** demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal *** total,1,035 genes associated with plant adaptive regulation for salt stress,radiation,and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population,of which 37.29% and 65.26% were detected by SVs and SNPs,*** genes such as FSD2,RGA1,and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV *** study highlights the importance of SVs in local adaptation;candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

关键词： climate change grape breeding local adaptation with gene flow salt tolerance viticulture Vitis

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Seasonal variation of mesoscale eddy intensity in the global ocean

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Acta Oceanologica Sinica 2024年第1期43卷 48-58页

作者： Yongcan Zu Yue Fang Shuangwen Sun Libao Gao Yang Yang Guijun Guo First Institute of Oceanography/key laboratory of marine Science and Numerical Modeling Ministry of Natural ResourcesQingdao 266061China laboratory for Regional Oceanography and Numerical Modeling Laoshan LaboratoryQingdao 266237China Shandong key laboratory of marine Science and Numerical Modeling Qingdao 266061China

Mesoscale eddies are a prominent oceanic phenomenon that plays an important role in oceanic mass transport and energy *** by rotational speed,the eddy intensity is one of the most fundamental properties of an ***,the seasonal spatiotemporal variation in eddy intensity has not been examined from a global ocean *** this study,we unveil the seasonal spatiotemporal characteristics of eddy intensity in the global ocean by using the latest satellite-altimetry-derived eddy trajectory data *** results suggest that the eddy intensity has a distinct seasonal variation,reaching a peak in spring while attaining a minimum in autumn in the Northern Hemisphere and the opposite in the Southern *** seasonal variation of eddy intensity is more intense in the tropical-subtropical transition zones within latitudinal bands between 15°and 30°in the western Pacific Ocean,the northwestern Atlantic Ocean,and the eastern Indian Ocean because baroclinic instability in these areas changes *** analysis found that the seasonal variation of baroclinic instability precedes the eddy intensity by a phase of 2–3 months due to the initial perturbations needing time to grow into mesoscale eddies.

关键词： seasonal variation mesoscale eddy intensity baroclinic instability global ocean

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Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control

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Plant Communications 2024年第2期5卷 243-260页

作者： Wen-Zhao Xie Yu-Yu Zheng Weidi He Fangcheng Bi Yaoyao Li Tongxin Dou Run Zhou Yi-Xiong Guo Guiming Deng Wenhui Zhang Min-Hui Yuan Pablo Sanz-Jimenez Xi-Tong Zhu Xin-Dong Xu Zu-Wen Zhou Zhi-Wei Zhou Jia-Wu Feng Siwen Liu Chunyu Li Qiaosong Yang Chunhua Hu Huijun Gao Tao Dong Jiangbo Dang Qigao Guo Wenguo Cai Jianwei Zhang Ganjun Yi Jia-Ming Song Ou Sheng Ling-Ling Chen 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 ResearchGuangzhou 510640China College of Informatics Huazhong Agricultural UniversityWuhan 430070China State key laboratory for conservation and Utilization of subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China College of Horticulture and Landscape Architecture Southwest UniversityChongqing 400715China

Bananas(Musa spp.)are one of the world’s most important fruit crops and play a vital role in food security for many developing *** banana cultivars are triploids derived from inter-and intraspecific hybrid-izations between the wild diploid ancestor species Musa acuminate(AA)and ***(BB).We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types,Plantain and Silk,and precisely characterize ancestral contributions by examining ancestry mosaics across the *** asymmetric evolution is observed in their subgenomes,which can be linked to frequent homol-ogous exchange *** reveal the genetic makeup of triploid banana cultivars and verify that subge-nome B is a rich source of disease resistance *** 58.5%and 59.4%of Plantain and Silk genes,respectively,are present in all three haplotypes,with>50%of genes being differentially expressed alleles in different *** observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4(Foc TR4),which con-firms that Plantain can initiate defense responses faster than ***,we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and *** study provides resources for better understanding the genomic architecture of culti-vated bananas and has important implications for Musa genetics and breeding.

关键词： bananas Plantain Silk asymmetric evolution homologous exchange Fusarium wilt

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Lipid concentration and composition in xylem sap of woody angiosperms from a tropical savanna and a seasonal rainforest

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Plant Diversity 2024年第1期46卷 126-133页

作者： Ling-Bo Huang Xinyi Guan Amy Ny Aina Aritsara Jun-Jie Zhu Steven Jansen Kun-Fang Cao State key laboratory for conservation and Utilization of subtropical Agro-bioresources Guangxi Key Laboratory of Forest Ecology and ConservationGuangxi UniversityDaxuedong Road 100NanningGuangxi 530004China Institute of Botany Ulm UniversityAlbert-Einstein-Allee 11Ulm89081Germany

Lipids may play an important role in preventing gas embolisms by coating nanobubbles in xylem *** studies on xylem sap lipids have been reported for temperate plants,and it remain unclear whether sap lipids have adaptational significance in tropical *** this study,we quantify the lipid composition of xylem sap for angiosperm species from a tropical savanna(seven species)and a seasonal rainforest(five species)using mass *** found that all twelve species studied contained lipids in their xylem sap,including galactolipids,phospholipids and triacylglycerol,with a total lipid concentration ranging from 0.09 to 0.26 nmol/*** was no difference in lipid concentration or composition between plants from the two sites,and the lipid concentration was negatively related to species’open vessel ***,savanna species showed little variation in lipid composition between the dry and the rainy *** results support the hypothesis that xylem sap lipids are derived from the cytoplasm of individual conduit cells,remain trapped inside individual conduits,and undergo few changes in composition over consecutive seasons.A xylem sap lipidomic data set,which includes 12 tropical tree species from this study and 11 temperate tree species from literature,revealed no phylogenetic signals in lipid composition for these *** study fills a knowledge gap in the lipid content of xylem sap in tropical trees and provides additional support for their common distribution in xylem sap of woody *** appears that xylem sap lipids have no adaptive significance.

关键词： Xylem sap Lipids tropical savanna tropical rainforest Vessels

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High-quality genome assemblies for two Australimusa bananas(Musa spp.)and insights into regulatory mechanisms of superior fiber properties

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Plant Communications 2024年第1期5卷 245-261页

作者： Run Zhou Shuo Wang Ni Zhan Weidi He Guiming Deng Tongxin Dou Xi-Tong Zhu Wen-Zhao Xie Yu-Yu Zheng Chunhua Hu Fangcheng Bi Huijun Gao Tao Dong Siwen Liu Chunyu Li Qiaosong Yang Lingqiang Wang Jia-Ming Song Jiangbo Dang Qigao Guo Ganjun Yi Ling-Ling Chen Ou Sheng 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 ResearchGuangzhou 510640China College of Informatics Huazhong Agricultural UniversityWuhan 430070China State key laboratory for conservation and Utilization of subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China College of Horticulture and Landscape Architecture Southwest UniversityChongqing 400715China

Bananas(Musa spp.)are monocotyledonous plants with high genetic diversity in the Musaceae family that are cultivated mainly in tropical and subtropical *** fruits are a popular food,and the plants themselves have diverse *** genetic groups(genomes)are thought to have contributed to current banana cultivars:Musa acuminata(A genome),Musa balbisiana(B genome),Musa schizocarpa(S genome),and species of the Australimusa section(T genome).However,the T genome has not been effectively ***,we present the high-quality TT genomes of two representative accessions,Abaca(Musa textilis),with high-quality naturalfiber,and Utafun(Musa troglodytarum,Fe’i group),with abundant *** the Abaca and Utafun assemblies comprise 10 pseudochromosomes,and their total genome sizes are 613 Mb and 619 Mb,*** genome analysis revealed that the larger size of the T genome is likely attributable to rapid expansion and slow removal of *** with those of Musa AA or BB accessions or sisal(Agava sisalana),Abacafibers exhibit superior mechanical properties,mainly because of their thicker cell walls with a higher content of cellulose,lignin,and *** of MusaCesA cellulose synthesis genes peaks earlier in Abaca than in AA or BB accessions during plant development,potentially leading to earlier cellulose accumulation during secondary cell wall *** Abaca-specific expressed gene MusaMYB26,which is directly regulated by MusaMYB61,may be an important regulator that promotes precocious expression of secondary cell wall ***,MusaWRKY2 and MusaNAC68,which appear to be involved in regulating expression of MusaLAC and MusaCAD,may at least partially explain the high accumulation of lignin in *** work contributes to a better understanding of banana domestica-tion and the diverse genetic resources in the Musaceae family,thus providing resources for Musa genetic improvement.

关键词： Australimusa bananas T genome Musaceae evolution structural variations fiber

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Evolution history dominantly regulates fine root lifespan in tree species across the world

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Forest Ecosystems 2024年第4期11卷 516-525页

作者： Xingzhao Huang Zhouying Lu Fangbing Li Yang Deng Fangfang Wan Quancheng Wang Fousseni Folega Jinsong Wang Zijian Guo Anhui Province key laboratory of Forest resources and Silviculture Anhui Agricultural UniversityHefei 230036China State key laboratory of subtropical Silviculture Zhejiang A&F UniversityHangzhou 311300China key laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesBeijing 100101China laboratory of Botany and Plant Ecology(LBEV) University of LomeTogo01PoBox 1515LomeTogo State key laboratory of Efficient Production of Forest resources Beijing Forestry UniversityBeijing 100083China School of Ecology and Nature conservation Beijing Forestry UniversityBeijing 100083China

Understanding the drivers of variations in fine root lifespan is key to informing nutrient cycling and productivity in terrestrial ***,the general patterns and determinants of forest fine root lifespan at the global scale are still *** compiled a dataset of 421 fine root lifespan observations from 76 tree species globally to assess phylogenetic signals among species,explored relationships between fine root lifespan and biotic and abiotic factors,and quantified the relative importance of phylogeny,root system structure and functions,climatic and edaphic factors in driving global fine root lifespan ***,fine root lifespan showed a clear phylogenetic signal,with gymnosperms having a longer fine root lifespan than *** root lifespan was longer for evergreens than deciduous ***(ECM)plants had an extended fine root lifespan than arbuscular mycorrhizal(AM)*** different climatic zones,fine root lifespan was the longest in the boreal zone,while it did not vary between the temperate and tropical *** root lifespan increased with soil depth and root ***,the analysis of relative importance indicated that phylogeny was the strongest driver influencing the variation in forest fine root lifespan,followed by soil clay content,root order,mean annual temperature,and soil depth,while other environmental factors and root traits exerted weaker *** results suggest that the global pattern of fine root lifespan in forests is shaped by the interplay of phylogeny,root traits and environmental *** findings necessitate accurate representations of tree evolutionary history in earth system models to predict fine root longevity and its responses to global changes.

关键词： Fine root lifespan Trees Phylogeny Root order Soil property Climatic factors

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Aboveground biomass stocks of species-rich natural forests in southern China are influenced by stand structural attributes,species richness and precipitation

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Plant Diversity 2024年第4期46卷 530-536页

作者： Wen-Hao Zeng Shi-Dan Zhu Ying-Hua Luo Wei Shi Yong-Qiang Wang Kun-Fang Cao State key laboratory for conservation and Utilization of subtropical Agro-Bioresources College of ForestryGuangxi UniversityNanning 530004China Guangxi key laboratory of Forest Ecology and conservation College of ForestryGuangxi UniversityNanning 530004China key laboratory of National Forestry and Grassland Administration on Biodiversity conservation in Karst Mountainous Areas of Southwestern China School of Life SciencesGuizhou Normal UniversityHuaxi College TownGui'an DistrictGuiyang 550025China

Forests,the largest terrestrial carbon sinks,play an important role in carbon sequestration and climate change *** forest attributes and environmental factors have been shown to impact aboveground biomass,their influence on biomass stocks in species-rich forests in southern China,a biodiversity hotspot,has rarely been *** this study,we characterized the effects of environmental factors,forest structure,and species diversity on aboveground biomass stocks of 30 plots(1 ha each) in natural forests located within seven nature reserves distributed across subtropical and marginal tropical zones in Guangxi,*** results indicate that forest aboveground biomass stocks in this region are lower than those in mature tropical and subtropical forests in other ***,we found that aboveground biomass was positively correlated with stand age,mean annual precipitation,elevation,structural attributes and species richness,although not with species *** we compared stands with the same basal area,we found that aboveground biomass stock was higher in communities with a higher coefficient of variation of diameter at breast *** findings highlight the importance of maintaining forest structural diversity and species richness to promote aboveground biomass accumulation and reveal the potential impacts of precipitation changes resulting from climate warming on the ecosystem services of subtropical and northern tropical forests in ***,many natural forests in southern China are not fully ***,their continued growth will increase their carbon storage over time.

关键词： subtropical forest Marginal tropical forest Aboveground biomass Species diversity Forest structural attribute Environment factor

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EupDB:An integrative and comprehensive functional genomics data hub for Euphorbiaceae plants

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Plant Communications 2024年第1期5卷 8-11页

作者： Jiazhi Liu Yan Li Jing Li Wen Chen Bangzhen Pan Aizhong Liu Zeng-Fu Xu Wei Xu Changning Liu CAS key laboratory of tropical Plant resources and Sustainable Use Yunnan Key Laboratory of Crop Wild Relatives OmicsXishuangbanna Tropical Botanical GardenChinese Academy of SciencesKunming 650223China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China key laboratory of Vascular Biology and Translational Medicine Medical SchoolHunan University of Chinese MedicineChangsha 410208China key laboratory for Forest resources conservation and Utilization in the Southwest Mountains of China Ministry of EducationSouthwest Forestry UniversityKunming 650224China State key laboratory for conservation and Utilization of subtropical AgroBioresources College of ForestryGuangxi UniversityNanning 530003China key laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China College of ForestryGuangxi UniversityNanning 530003China Germplasm Bank of Wild Species Yunnan Key Laboratory of Crop Wild Relatives OmicsKunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina

Dear Editor,Euphorbiaceae is one of the largest plant families,with nearly 218 genera and 6745 species,and includes many economically and medicinally important ***,cassava(Manihot esculenta)is well known as the"king of starches"and is the fourth most important food source in the tropics;rubber tree(Hevea brasiliensis)is a principal source of natural rubber for over 50000 industrial products worldwide;castor bean(Ricinus communis)is a globally important non-edible oilseed crop and the only commercial source of industrially valuable hydroxyl fatty acids.

关键词： esculenta) comprehensive rubber

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A new infrageneric classification of Gastrochilus(Orchidaceae:Epidendroideae)based on molecular and morphological data

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Plant Diversity 2024年第4期46卷 435-447页

作者： Jun-Yi Zhang Yue-Hong Cheng Min Liao Yu Feng Sen-Long Jin Ting-Mei He Hai He Bo Xu China-Croatia“Belt and Road”Joint laboratory on Biodiversity and Ecosystem Services CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan ProvinceChengdu Institute of BiologyChinese Academy of SciencesP.O.Box 416Chengdu 610041SichuanChina College of Life Sciences Chongqing Normal UniversityChongqing 401331China Wolong National natural Reserve Administration Bureau Wenchuan 623006SichuanChina University of Chinese Academy of Sciences Beijing 100049China

Gastrochilus is an orchid genus containing 73 species of mainly epiphytic on trees or rocks in mountain forests of tropical and subtropical *** phylogenetic analyses and morphological assessments have failed to produce a well-resolved phylogeny at the infrageneric *** the present study,a new infrageneric classification of Gastrochilus is proposed based on thoroughly morphological and phylogenetic analyses based on 52 *** phylogenetic analysis divided the genus into six sections including three new sections,***,*** and *** also reinstate *** to the specific ***,two new species,*** Jun ***,***&Yue *** and *** Jun ***,***&Yue ***,are described and illustrated.A key to six sections of the genus is presented.

关键词： Gastrochilus Phylogeny Character evolution Taxonomy New species

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Slc43a2^(+)T cell metastasis from spleen to brain in RGNNV infected teleost

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Science China(Life Sciences) 2024年第4期67卷 733-744页

作者： Qing Wang Yali Liu Minlin Zhang Min Yang Jiantao Liang Xiaoling Zuo Shaowen Wang Xianze Jia Huihong Zhao Han Jiang Qiang Lin Qiwei Qin College of marine Sciences South China Agricultural UniversityGuangzhou 510642China CAS key laboratory of tropical marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Nansha-South China Agricultural University Fishery Research Institute Guangzhou 511457China Joint University laboratory of Guangdong Province Hong Kong and Marco Region on Marine Bioresource Conservation and ExploitationGuangzhou 510642China University of Chinese Academy of Sciences Beijing 100101China

The origin of T cells in the teleost's brain is *** viewing the central nervous system(CNS)as immune privileged has been widely accepted,previous studies suggest that T cells residing in the thymus but not in the spleen of the teleost play an essential role in communicating with the peripheral ***,we identified nine T cell subpopulations in the thymus and spleen of orange-spotted grouper(Epinephelus coioices)through single-cell RNA-sequencing *** viral CNS infection with red-spotted grouper nervous necrosis virus(RGNNV),the number of slc43a2^(+)T cells synchronously increased in the spleen and *** the infection tests in asplenic zebrafish(tlx1^▲zebrafish model),no increase in the number of slc43a2^(+)T cells was observed in the ***-cell transcriptomic analysis indicated that slc43a2^(+)T cells mature and functionally differentiate within the spleen and then migrate into the brain to trigger an immune *** study suggests a novel route for T cell migration from the spleen to the brain during viral infection in fish.

关键词： central nervous system slc43a2^(+)T cell RGNNV T cell migration teleost

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