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Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

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Zoological Research 2024年第1期45卷 160-175页

作者： Yu-Ran Li Zheng-Wei Wang Richard T.Corlett Wen-Bin Yu Yunnan Key Laboratory for the conservation of tropical Rainforests and Asian Elephants&Center for Integrative conservation Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China CAS Key Laboratory of tropical forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China Southeast Asia Biodiversity Research institute Chinese Academy of SciencesMenglaYunnan 666303China University of Chinese Academy of Sciences Shijingshan DistrictBeijing 100049China

The insect mitogenome is typically a compact circular molecule with highly conserved gene ***,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different *** synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing ***,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect *** provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population *** analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and *** inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee *** evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial *** finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome *** conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.

关键词： Social bees Phylogeny Mitogenome structure Gene rearrangement Inverted repeats

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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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Natural forests exhibit higher organic carbon concentrations and recalcitrant carbon proportions in soil than plantations:a global data synthesis

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Journal of forestry Research 2024年第5期35卷 131-141页

作者： Xiuqing Nie Hui Wang Jian Wang Shirong Liu Ecology and Nature conservation institute Chinese Academy of ForestryKey Laboratory of Forest Ecology and Environment of National Forestry and Grassland AdministrationNo.2 DongxiaofuHaidian DistrictBeijing 100091People’s Republic of China

Different chemical compositions of soil organic carbon(SOC)affect its persistence and whether it signifi-cantly differs between natural forests and plantations remains *** synthesizing 234 observations of SOC chemical compositions,we evaluated global patterns of concentra-tion,individual chemical composition(alkyl C,O-alkyl C,aromatic C,and carbonyl C),and their distribution *** results indicate a notably higher SOC,a markedly larger proportion of recalcitrant alkyl C,and lower easily decomposed carbonyl C proportion in natural ***-ever,SOC chemical compositions were appreciably more evenly distributed in *** on the assumed con-ceptual index of SOC chemical composition evenness,we deduced that,compared to natural forests,plantations may have higher possible resistance to SOC decomposition under *** tropical regions,SOC levels,recalcitrant SOC chemical composition,and their distributed evenness were significantly higher in natural forests,indicating that SOC has higher chemical stability and possible resistance to *** factors had minor effects on alkyl C in forests globally,while they notably affected SOC chemi-cal composition in tropical *** could contribute to the differences in chemical compositions and their distrib-uted evenness between plantations and natural stands.

关键词： Global data synthesis Natural forest Plantations Soil organic carbon Soil organic carbon chemical composition

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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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Paleogene integrative stratigraphy,biotas,and paleogeographical evolution of the Qinghai-Tibetan Plateau and its surrounding areas

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Science China Earth Sciences 2024年第4期67卷 1290-1325页

作者： Jia LIU Ai SONG Lin DING Tao SU Zhekun ZHOU CAS Key Laboratory of tropical forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla 666303China State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjing 210008China institute of Paleontology Yunnan UniversityKunming 650500China State Key Laboratory of Tibetan Plateau Earth System Environment and Resources(TPESER)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China

The Paleogene is a crucial period when terrestrial and marine ecosystems recovered from major disruptions and gradually approached their modern *** the Qinghai-Tibetan Plateau and its surrounding regions,the Paleogene also represents a significant phase of tectonic evolution in the Qinghai-Tibetan Plateau-Himalaya orogeny,reorganization of Asian climates,and evolution of *** to limitations in research conditions and understanding,there are still many controversies regarding stratigraphic divisions in the Qinghai-Tibetan Plateau and its surrounding *** recent years,extensive studies on sedimentary petrology,magnetostratigraphy,and isotope dating have been conducted in the *** fossils have been discovered and reported,contributing to a more systematic understanding of *** studies have laid a solid foundation for the comprehensive investigation of the stratigraphy,biotas and paleogeographic evolution of the Qinghai-Tibetan Plateau and its surrounding regions during the *** this paper,we integrate recent research on fossils,isotopic dating,magnetostratigraphy,and geochemistry to refine the stratigraphic divisions and correlation framework of different tectonic units in the region,building upon previous *** the Second Tibetan Plateau Scientific Expedition and Research,the knowledge of Paleogene floras has gradually *** paper discusses the biostratigraphic significance of extinct and newly appeared taxa based on the latest dating results of these plant *** new understanding of fossil species such as the“Eucalyptus”and Arecaceae establishes connections between the Paleogene flora of the Qinghai-Tibetan region and the biotas of Gondwana,specifically Oceania and South *** evolutionary history of key taxa near the Yarlung Zangbo suture zone indicates that the collision between the Indian and Eurasian plates occurred approximately 65-54 *** reconstructions,based o

关键词： Qinghai-Tibetan Plateau Fossils Biostratigraphy Paleoenvironment Paleogeography Paleogene

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Tracking the Confiscated Green Sea Turtles in the South China Sea:Where Did They Come From?Where Will They Go?

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Asian Herpetological Research 2024年第3期15卷 173-182页

作者： Min CHEN Tong HUANG Dayi NIE Liu LIN Fang CHEN Jing WANG Jinyan YANG Jing ZHANG Tong LIU Yiqiong CUI School of Life Sciences Institute of Eco-ChongmingShanghai Institute of Wildlife EpidemicsEast China Normal UniversityShanghai 200241China Hainan institute of East China Normal University Sanya 572025HainanChina 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 UniversityHaikou 571158HainanChina Aquatic Wildlife conservation Branch of China Wildlife conservation Association Beijing 100013China Society of Entrepreneurs and Ecology Beijing 100012China Commonwealth Scientific and Industrial Research Organisation Canberra ACT 2601Australia

The population of the green sea turtle(Chelonia mydas)is under decline,threatened by bycatch and illegal acquisition despite worldwide protection ***,the confiscation of illegally acquired sea turtles could aid in tracking their origin and movement patterns,crucial for effective conservation *** satellite tracking and genetic analysis offers an opportunity to investigate the relationship between the origins and migration directions of green sea turtles in the western ***,we applied two methods to investigate the spatial ecology of 18 green turtles caught as bycatch in the South China *** results revealed the genetic origins and diverse movements of the *** Mixed Stock Analysis(MSA)suggested that these turtles originated from the rookery of the Xisha Islands(49.6%),central Ryukyu(24.6%),NE Borneo(8%),and the Sulu Sea(5.2%),with other rookeries in meagre proportions(conservation efforts of neighbouring countries in the South China Sea.

关键词： conservation genetics green sea turtle(Chelonia mydas) movement rookery satellite tracking

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Fine-mapping and primary analysis of candidate genes associated with seed coat color in mung bean(Vigna radiata L.)

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Journal of Integrative Agriculture 2024年第8期23卷 2571-2588页

作者： Qian Wang Huimin Cao Jingcheng Wang Zirong Gu Qiuyun Lin Zeyan Zhang Xueying Zhao Wei Gao Huijun Zhu Hubin Yan Jianjun Yan Qingting Hao Yaowen Zhang College of Agronomy Shanxi Agricultural UniversityTaiyuan 030031China 2 tropical Crops Genetic Resources institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

Seed coat color affects the appearance and commodity quality of mung beans(Vigna radiata L.).The substances that affect mung bean seed coat color are mainly flavonoids,which have important medicinal *** the seed coat color gene in mung beans would facilitate the development of new varieties and improve their *** this study,an F2 mapping population consisting of 546 plants was constructed using Jilv9(black seed coat)and BIS9805(green seed coat).Using bulk segregated analysis(BSA)sequencing and kompetitive allele-specific PCR(KASP)markers,the candidate region related to seed coat color was finally narrowed to 0.66 Mb on chromosome(Chr.)4 and included eight candidate *** transcriptome and metabolome analyses showed that three of the eight candidate genes(LOC106758748,LOC106758747,and LOC106759075)were differentially expressed,which may have caused the differences in flavonoid metabolite content between Jilv9 and *** findings can provide a research basis for cloning the genes related to seed coat color and accelerate molecular markerassisted selection breeding in mung beans.

关键词： mung bean seed coat color bulk segregated analysis sequencing transcriptome metabolism flavonoids

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A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

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National Science Review 2024年第6期11卷 105-118页

作者： Xiaoxia Li Xiaofan Dai Huiying He Yang Lv Longbo Yang Wenchuang He Congcong Liu Hua Wei Xiangpei Liu Qiaoling Yuan Xianmeng Wang Tianyi Wang Bintao Zhang Hong Zhang Wu Chen Yue Leng Xiaoman Yu Hongge Qian Bin Zhang Mingliang Guo Zhipeng Zhang Chuanlin Shi Qianqian Zhang Yan Cui Qiang Xu Xinglan Cao Dandan Chen Yongfeng Zhou Qian Qian Lianguang Shang 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 Sciences Rice Research institute Shenyang Agricultural University Yazhouwan National Laboratory State Key Laboratory of Rice Biology China National Rice Research Institute National Key Laboratory of tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural Sciences

Transposable elements(TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing *** the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms(SNPs), such as Os Rboh B, and validated Os Rboh B's relative expression activity using a dual-Luciferase(LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

关键词： transposable element super pan-genome pan-TE rice

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Toward the generation of pure coral genomes with experimental and bioinformatic improvements

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The Innovation 2024年第4期5卷 30-32页

作者： Yisi Hu Zhiwei Zhang Shuyan Sun Youfang Sun Hui Huang Wenliang Zhou Fuwen Wei Center for Evolution and conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)Guangzhou 511458China Jiangxi Provincial Key Laboratory of conservation Biology College of ForestryJiangxi Agricultural UniversityNanchang 330029China Key Laboratory of Animal Ecology and conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of tropical Marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China

Stony corals,the primary architects of coral reef ecosystems,are largely underrepresented in omics studies despite their *** presence of endosymbiotic Symbiodiniaceae algae complicates the extraction of pure coral DNA,posing a challenge for genomic ***,we devised a comprehensive methodological framework that incorporates various experimental treatments to achieve 99%purity in coral DNA extraction and a robust bioinformatics pipeline to guarantee the assembly of high-quality,contamination-free coral *** of our framework using Acropora millepora samples demonstrated its efficacy and superiority in obtaining high-quality pure coral genomes using easily accessible adult *** integrated framework serves as a critical foundation for largescale genome-enabled research on stony corals,providing insight into coral evolution and conservation.

关键词： coral guarantee purity

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Identification of a natural PLA2 inhibitor from the marine fungus Aspergillus sp.c1 for MAFLD treatment that suppressed lipotoxicity by inhibiting the IRE-1a/XBP-1s axis and JNK signaling

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Acta Pharmaceutica Sinica B 2024年第1期14卷 304-318页

作者： Yong Rao Rui Su Chenyan Wu Xingxing Chai Jinjian Li Guanyu Yang Junjie Wu Tingting Fu Zhongping Jiang Zhikai Guo Congjun Xu Ling Huang Key Laboratory of tropical Biological Resources of Ministry of Education School of Pharmaceutical SciencesHainan UniversityHaikou 570200China Hainan Key Laboratory of tropical Microbe Resources Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural Sciences&Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agricultural ResourcesHaikou 571101China School of Pharmaceutical Sciences Guangdong Provincial Key Laboratory of New Drug Design and EvaluationSun Yat-sen UniversityGuangzhou 510275China Laboratory Animal Center of Guangdong Medical University Dongguan 523808China

Lipotoxicity is a pivotal factor that initiates and exacerbates liver injury and is involved in the development of metabolic-associated fatty liver disease(MAFLD).However,there are few reported lipotoxicity ***,we identified a natural anti-lipotoxicity candidate,HN-001,from the marine fungus Aspergillus ***-001 dose-and time-dependently reversed palmitic acid(PA)-induced hepatocyte *** protection was associated with IRE-1a-mediated XBP-1 splicing inhibition,which resulted in suppression of XBP-1s nuclear translocation and transcriptional *** of XBP-1s attenuated lipotoxicity,but no additional ameliorative effect of HN-001 on lipotoxicity was observed in XBP-1s knockdown ***,the ER stress and lipotoxicity amelioration was associated with *** HN-001 and the PLA2 inhibitor MAFP inhibited PLA2 activity,reduced lysophosphatidylcholine(LPC)level,subsequently ameliorated *** contrast,overexpression of PLA2 caused exacerbation of lipotoxicity and weakened the anti-lipotoxic effects of ***,HN-001 treatment suppressed the downstream pro-apoptotic JNK *** vivo,chronic administration of HN-001(i.p.)in mice alleviated all manifestations of MAFLD,including hepatic steatosis,liver injury,inflammation,and *** effects were correlated with PLA2/IRE-1a/XBP-1s axis and JNK signaling *** data indicate that HN-001 has therapeutic potential for MAFLD because it suppresses lipotoxicity,and provide a natural structural basis for developing anti-MAFLD candidates.

关键词： Lipotoxicity MAFLD ER stress IRE-1a XBP-1s JNK PLA2

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