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Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 51-65页

作者： Binzhong Wang Bin Wu Xueqing Liu Yacheng Hu Yao Ming Mingzhou Bai Juanjuan Liu Kan Xiao Qingkai Zeng Jing Yang Hongqi Wang Baifu Guo Chun Tan Zixuan Hu Xun Zhao Yanhong Li Zhen Yue Junpu Mei Wei Jiang Yuanjin Yang Zhiyuan Li Yong Gao Lei Chen Jianbo Jian Hejun Du Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes Yichang 443100China Chinese Sturgeon Research Institute China Three Gorges CorporationYichang 443100China Yangtze River Biodiversity Research Center China Three Gorges CorporationWuhan 430014China bgi-Shenzhen Shenzhen 518083China bgi Genomics BGI-ShenzhenShenzhen 518083China Department of Biotechnology and Biomedicine Technical University of DenmarkLyngby 2800Denmark River Basin Complex Administration Center China Three Gorges CorporationYichang 443100China bgi-sanya BGI-ShenzhenSanya 572025China Yangtze Eco-Environment Engineering Research Center China Three Gorges CorporationBeijing 100038China

The order Acipenseriformes,which includes sturgeons and paddlefishes,represents“living fossils”with complex genomes that are good models for understanding whole-genome duplication(WGD)and ploidy evolution in ***,we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis(Chinese sturgeon),a critically endangered species that also represents a poorly understood ploidy group in *** results show that *** is a complex autooctoploid species containing four kinds of octovalents(8n),a hexavalent(6n),two tetravalents(4n),and a divalent(2n).An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs,and further provides insights into the timing of its ploidy *** study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes.

关键词： Chinese sturgeon Whole-genome sequencing Autooctoploid Polyploidization and diploidization Whole-genome duplication

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Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals(Octocorallia:Alcyonacea):Insights into slow evolution and adaptation to extreme deep-sea environments

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Zoological Research 2024年第1期45卷 215-225页

作者： Zhan-Fei Wei Kai-Wen Ta Nan-Nan Zhang Shan-Shan Liu Liang Meng Kai-Qiang Liu Chong-Yang Cai Xiao-Tong Peng Chang-Wei Shao National Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China bgi-Qingdao BGI-ShenzhenQingdaoShandong 266555China Institute of Deep-Sea Science and Engineering Chinese Academy of SciencesSanyaHainan 572000China

A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomic characteristics,morphological examination,and sclerite scanning electron microscopy,the samples were categorized into four suborders(Calcaxonia,Holaxonia,Scleraxonia,and Stolonifera),and identified as 9 possible new cold-water coral *** of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial *** nonsynonymous(Ka)to synonymous(Ks)substitution ratio(Ka/Ks)suggested that the 14 protein-coding genes(PCGs)were under purifying selection,likely due to specific deep-sea environmental *** analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b)and DNA mismatch repair protein(mutS)may be influenced by environmental factors in the context of deep-sea species *** study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.

关键词： Mitochondrial genome Alcyonacea Ka/Ks evolution Environmental factors

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Precision regulation of plant aromatic amino acid homeostasis

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Science China(Life Sciences) 2024年第6期67卷 1316-1317页

作者： Jie Luo Yazhouwan National Laboratory(YNL) Sanya 572025China School of Breeding and Multiplication(sanya Institute of Breeding and Multiplication) Hainan UniversitySanya 572025China

The aromatic amino acids(AAAs)phenylalanine(Phe),tyrosine(Tyr),and tryptophan(Trp)are not only building blocks of proteins,but also precursors of numerous primary and specialized metabolites(Schenck and Maeda,2018).For instance,Trp is a precursor of the phytohormone auxin and the plant defense compounds indole glucosinolates,while Phe serves as a precursor of lignin,coumarin and *** plant natural products such as morphine and vitamin E are derived from Tyr,and have been employed in human medicine and nutrition(Schenck and Maeda,2018;Wu et al.,2022;Yokoyama et al.,2021).

关键词： aromatic instance coumarin

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DAIS: a method for identifying spatial domains based on density clustering of spatial omics data

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Journal of Genetics and Genomics 2024年第8期51卷 884-887页

作者： Qichao Yu Ru Tian Xin Jin Liang Wu College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China bgi Research ShenzhenGuangdong 518083China BGI ResearchChongqing 401329China bgi Research ShenzhenGuangdong 518083China bgi Research Chongqing 401329China

In multicellular organisms,the spatial arrangement of cells profoundly influences the biological functions of tissues,underscoring the importance of identifying spatial domains in *** advancements in spatial omics,particularly spatial transcriptomics(ST)(Bressan et al.,2023),have enhanced our understanding of tissue spatial organization(Zhang et al.,2022;Tian et al.,2023).

关键词： arrangement identifying domains

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Cross-resistance and genetics of field-evolved resistance to chlorfenapyr in Plutella xylostella

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Insect Science 2024年第2期31卷 533-541页

作者： Cheng Qian Jialin Li Shuwen Wu Yihua Yang Yidong Wu Xingliang Wang sanya Institute of Nanjing Agricultural Universty SanyaHainanChinaand College of Plant Protection Nanjing Agricultural UniversNanjingChina

Chlorfenapyr is a broad-spectrum halogenated pyrrole insecticide with a unique mode of *** to the misuse and overuse of this chemical,resistance has been reported in several arthropods,including Plutella xylostella,which is one of the most destructive insect pests afflicting crucifers worldwide.A better understanding of the cross-resistance and genetics of field-evolved chlorfenapyr resistance could effectively guide resistance management ***,the chlorfenapyr resistance of a fieldderived population of P xylostella was introgressed into the susceptible IPP-S strain using a selection-assisted multigenerational backcrossing *** constructed nearisogenic strain,TH-BCsF2,shared 98.4%genetic background with the recurrent parent IPP-S *** TH-BCsF2 strain showed 275-fold resistance to chlorfenapyr,but no significant cross-resistance to spinosad,abamectin,chlorpyrifos,β-cypermethrin,indoxacarb,chlorantraniliprole,or broflanilide(no more than 4.2-fold).Genetic analysis revealed that resistance was autosomal,incompletely dominant,and conferred by 1 major gene or a few tightly linked *** synergism of metabolic inhibitors(PBO,DEM,and DEF)to chlorfenapyr was very weak(<1.7-fold),and the metabolic enzyme activities in the TH-BCsF2 strain were not significantly elevated compared with the IPP-S *** results enhances our understanding of the genetic traits of chlorfenapyr resistance,and provides essential information for improving resistance management strategies.

关键词： chlorfenapyr cross-resistance mode of inheritance near-isogenic line Plutellaxylostella

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Enhancing Dense Small Object Detection in UAV Images Based on Hybrid Transformer

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Computers, Materials & Continua 2024年第3期78卷 3993-4013页

作者： Changfeng Feng Chunping Wang Dongdong Zhang Renke Kou Qiang Fu Shijiazhuang Campus People Liberation Army Engineering UniversityShijiazhuang050003China School of Information and Intelligent Engineering Sanya UniversitySanya572000China

Transformer-based models have facilitated significant advances in object ***,their extensive computational consumption and suboptimal detection of dense small objects curtail their applicability in unmanned aerial vehicle(UAV)*** these limitations,we propose a hybrid transformer-based detector,H-DETR,and enhance it for dense small objects,leading to an accurate and efficient ***,we introduce a hybrid transformer encoder,which integrates a convolutional neural network-based cross-scale fusion module with the original encoder to handle multi-scale feature sequences more ***,we propose two novel strategies to enhance detection performance without incurring additional inference *** filter is designed to cope with the dense clustering inherent in drone-captured images by counteracting similar queries with a training-aware non-maximum *** denoising learning is a novel enhancement method inspired by adversarial learning,which improves the detection of numerous small targets by counteracting the effects of artificial spatial and semantic *** experiments on the VisDrone and UAVDT datasets substantiate the effectiveness of our approach,achieving a significant improvement in accuracy with a reduction in computational *** method achieves 31.9%and 21.1%AP on the VisDrone and UAVDT datasets,respectively,and has a faster inference speed,making it a competitive model in UAV image object detection.

关键词： UAV images transformer dense small object detection

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Coupling of reduced inorganic fertilizer with plant-based organic fertilizer as a promising fertilizer management strategy for colored rice in tropical regions

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Journal of Integrative Agriculture 2024年第1期23卷 93-107页

作者： Tingcheng Zhao Aibin He Mohammad Nauman Khan Qi Yin Shaokun Song Lixiao Nie Research Center for Physiology and Ecology and Green Cultivation of Tropical Crops School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication)Hainan UniversitySanya 572000China

Colored rice is a type of high-quality,high-added-value rice that has attracted increasing attention in recent *** use of large amounts of inorganic nitrogen fertilizer in rice fields results in low fertilizer use efficiency and high environmental *** fertilizer is a promising way to improve soil quality and sustain high ***,most studies focus on the effect of animal-based organic *** effects of different ratios of plantbased organic fertilizer and inorganic fertilizer on the grain yield and quality of colored rice have rarely been ***,a two-year field experiment was conducted in 2020 and 2021 to study the effects of replacing inorganic N fertilizers with plant-based organic fertilizers on the yield,nitrogen use efficiency(NUE),and anthocyanin content of two colored rice varieties in a tropical region in *** experimental treatments included no nitrogen fertilization(T1),100% inorganic nitrogen fertilizer(T2),30%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T3),60%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T4),and 100% plantbased organic fertilizer(T5).The total nitrogen provided to all the treatments except T1 was the same at 120 kg *** results showed that the T3 treatment enhanced the grain yield and anthocyanin content of colored rice by increasing nitrogen use efficiency compared with *** average,grain yields were increased by 9 and 8%,while the anthocyanin content increased by 16 and 10% in the two colored rice varieties under T3 across the two years,respectively,as compared with *** study of the residual effect of partial substitution of inorganic fertilizers showed that the substitution of inorganic fertilizer with plant-based organic fertilizer improved the soil physiochemical properties,and thus increased the rice grain yield,in the subsequent *** highest grain yield of the subsequent rice crop was observe

关键词： colored rice organic fertilizer soil quality grain yield anthocyanin

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Piezoelectric composite hydrogel with wireless electrical stimulation enhances motor functional recovery of spinal cord injury

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Journal of Materials Science & Technology 2024年第5期172卷 228-239页

作者： Zehao Li Guanlin Li Xinyu Wang Zheng Zhao State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of TechnologyWuhan 430070China sanya Science and Education Innovation Park of Wuhan University of Technology Sanya 572000China

Electrical stimulation(ES)can restore motor function after spinal cord injury(SCI).However,traditional intraspinal ES has many disadvantages,such as the need for a complex circuitry device,an external power source,and a second surgery to remove the *** materials have received increasing at-tention due to their potential to convert ambient mechanical energy into ES without an external power source or implantation of ***,a novel polydopamine(PDA)coated barium titanate(BaTiO_(3))nanoparticles(BaTiO_(3)@PDA)incorporated silk fibroin(SF)hydrogel(SFBT)was *** SFBT hy-drogel was crosslinked by horseradish peroxidase(HRP)/hydrogel peroxide(H_(2)O_(2))to integrate the piezo-electric potency of BaTiO_(3)with the thermal sensitivity of HRP/H_(2)O_(2)for SCI *** hydrogel con-taining 5%(w/v)BaTiO_(3)@PDA nanoparticles(SFBT-5),which was selected for in vivo study,exhibited a short gelation time(5 min),suitable storage modulus(925±35 Pa),and wireless ES(average current of 124 nA).Moreover,Basso-Beattie-Bresnahan(BBB)scores test and footprint analysis demonstrated that the SFBT-5 hydrogel successfully enhanced motor functional recovery of *** histopathological assess-ments,the SFBT-5 hydrogel significantly accelerated spinal cord healing,as indicated by smaller lesion cavities(∼16.7%of the SCI group).Meanwhile,the SFBT-5 hydrogel accelerated neurogenesis,facilitated axon regrowth and synapse formation,and promoted ***,this study highlights the potential of piezoelectric hydrogels for SCI regeneration.

关键词： Silk fibroin Barium titanate Piezoelectric hydrogel Spinal cord injury Electrical stimulation

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A widely targeted metabolite modificomics strategy for modified metabolites identification in tomato

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Journal of Integrative Plant Biology 2024年第4期66卷 810-823页

作者： Jun Yang Ridong Chen Chao Wang Chun Li Weizhen Ye Zhonghui Zhang Shouchuang Wang School of Breeding and Multiplication(sanya Institute of Breeding and Multiplication) Hainan UniversitySanya 572025China School of Tropical Agriculture and Forestry Hainan UniversityHaikou 572208China

The structural and functional diversity of plant metabolites is largely created via chemical modification of a basic ***,metabolite modifications in plants have still not been thoroughly investigated by metabolomics *** this study,a widely targeted metabolite modificomics(WTMM)strategy was developed based on ultra-high performance liquid chromatography-quadrupole-linear ion trap(UHPLC-Q-Trap)and UHPLC-Q-Exactive-Orbitrap(UHPLC-QE-Orbitrap),which greatly improved the detection sensitivity and the efficiency of identification of modified metabolites.A metabolite modificomics study was carried out using tomato as a model,and over 34,000 signals with MS2 information were obtained from approximately 232 neutral loss *** metabolite profiling was also performed by utilizing high-resolution mass spectrometry data to annotate a total of 2,118 metabolites with 125 modification types;of these,165 modified metabolites were identified in this ***,the WTMM database was used to assess diseased tomato tissues and 29 biomarkers were *** summary,the WTMM strategy is not only capable of large-scale detection and quantitative analysis of plant-modified metabolites in plants,but also can be used for plant biomarker development.

关键词： LC-MS metabolic diversity metabolite modificomics modified groups tomato

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A chromosome-level genome of electric catfish(Malapterurus electricus)provided new insights into order Siluriformes evolution

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Marine Life Science & Technology 2024年第1期6卷 1-14页

作者： Meiru Liu Yue Song Suyu Zhang Lili Yu Zengbao Yuan Hengjia Yang Mengqi Zhang Zhuocheng Zhou Inge Seim Shanshan Liu Guangyi Fan Huanming Yang College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China bgi-Qingdao BGI-ShenzhenQingdao 266555China bgi-Shenzhen Shenzhen 518083China Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association Beijing 100125China Integrative Biology Laboratory College of Life SciencesNanjing Normal UniversityNanjing 210023China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China

The electric catfish(Malapterurus electricus),belonging to the family Malapteruridae,order Siluriformes(Actinopterygii:Ostariophysi),is one of the six branches that has independently evolved electrical *** assembled a 796.75 Mb *** genome and anchored 88.72%sequences into 28 *** family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate *** evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like(arhgef4),which is associated with G-protein coupled receptor(GPCR)signaling pathway,underwent adaptive parallel *** identification suggests visual degradation in catfishes,and an important role for taste in environmental *** findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes.

关键词： Electric fish Karyotype analysis Convergent evolution Environmental adaptation Historical effective population size

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