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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 organs.We assembled a 796.75 Mb M.electricus genome and anchored 88.72%sequences into 28 chromosomes.Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors.Convergent 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 evolution.Gene identification suggests visual degradation in catfishes,and an important role for taste in environmental adaptation.Our 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

Lactobacillus melliventris promotes hive productivity and immune functionality in Bombus terrestris performance in the greenhouse

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Insect Science 2024年第3期31卷 911-926页

作者： Qianhui Yu Yan Liu Shanshan Liu Shaogang Li Yifan Zhai Qingchao Zhang Li Zheng Hao Zheng Yifan Zhai Xiaofei Wang Insttute of Plant Protection Shandong Academy of Agricultural SciencesJinanChina Key Laboratory of Natural Enemies Insects Ministry of Agriculture and Rural AffairsJinanChina College of Food Science and Nutritional Engineering China Agricultural UniversityBeijingChina bgi-Qingdao BGI-ShenzhenQingdaoShandongChina

Bumblebees are important pollinators in agricultural ecosystems,but their abundance is declining globally.There is an urgent need to protect bumblebee health and their pollination services.Bumblebees possess specialized gut microbiota with potential to be used as probiotics to help defend at-risk bumblebee populations.However,evidence for probiotic benefits on bumblebees is lacking.Here,we evaluated how supplementation with Lactobacillus melliventris isolated from bumblebee gut affected the colony development of Bombus terrestris.This native strain colonized robustly and persisted long-term in bumblebees,leading to a significantly higher quality of offspring.Subsequently,the tyrosine pathway was upregulated in the brain and fat body,while the Wnt and mTOR pathways of the gut were downregulated.Notably,the field experiment in the greenhouse revealed the supplementation of L.melliventris led to a 2.5-fold increase in the bumblebee survival rate and a more than 10%increase in the number of flowers visited,indicating a better health condition and pollination ability in field conditions.Our study represents a first screening for the potential use of the native gut member,L.melliventris,as probiotic strains in hive supplement for bumblebee breeding,which may be a practical approach to improve immunity and hive health.

关键词： Bombus terrestris gut microbiota immunity Lactobacillus melliventris transcriptome

Sequencing and analysis of the giant panda genome

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Science China(Life Sciences) 2010年第8期53卷 1047-1048页

作者： YANG HuanMing bgi-Shenzhen (beijing Genomics Institute Shenzhen), Shenzhen 518083, China bgi-Shenzhen (beijing Genomics Institute Shenzhen) Shenzhen China

The giant panda (Ailuropoda melanoleuca) is loved all over the world and is considered a symbol of China, as illustrated by its being one of the

关键词： Sequencing and analysis of the giant panda genome

Maize gets an iron boost:Biofortification breakthrough holds promise to combat iron deficiency

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Journal of Integrative Plant Biology 2024年第4期66卷 635-637页

作者： Sunil Kumar Sahu State Key Laboratory of Agricultural Genomics Key Laboratory of GenomicsMinistry of AgricultureBGI ResearchShenzhen 518083China bgi Research Wuhan 430074China

Micronutrient deficiencies affect more than two billion people worldwide,resulting in poor health,developmental issues,and even death.Iron deficiency is one of the most prevalent micronutrient deficiencies worldwide a... 详细信息

关键词： population breakthrough holds

Theoretical investigations on the growth of graphene by oxygenassisted chemical vapor deposition

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Nano Research 2024年第6期17卷 4645-4650页

作者： Xiaoli Sun Chaojie Yu Yujia Yang Zhihao Li Jianjian Shi Wanjian Yin Zhongfan Liu beijing Graphene Institute(bgi) Beijing 100095China School of Physics and Electronics Shandong Normal UniversityJinan 250014China College of Energy Soochow Institute for Energy and Materials InnovationsLight Industry Institute of Electrochemical Power SourcesSUDA-BGI Collaborative Innovation CenterSoochow UniversitySuzhou 215006China School of Electronic Engineering Chengdu Technological UniversityChengdu 611730China Center for Nanochemistry Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China

Recently,graphene has drawn considerable attention in the field of electronics,owing to its favorable conductivity and high carrier mobility.Crucial to the industrialization of graphene is its high-quality microfabrication via chemical vapor deposition.However,many problems remain in its preparation,such as the not fully understood cracking mechanism of the carbon source,the mechanism of its substrate oxidation,and insufficient defect repair theory.To help close this capability gap,this study leverages density functional theory to explore the role of O in graphene growth.The effects of Cu substrate oxidation on carbon source cracking,nucleation barriers,crystal nucleus growth,and defect repairs are discussed.OCu was found to reduce energy change during dehydrogenation,rendering the process easier.Moreover,the adsorbed O in graphene or its Cu substrate can promote defect repair and edge growth.

关键词： density functional theory oxygen-assisted graphene growth chemical vapor deposition Cu substrate

The spatial transcriptomic landscape of human gingiva in health and periodontitis

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Science China(Life Sciences) 2024年第4期67卷 720-732页

作者： Zongshan Shen Ran Zhang Yunjia Huang Jiayao Chen Mengjun Yu Chunhua Li Yong Zhang Lingling Chen Xin Huang Jichen Yang Zhengmei Lin Songlin Wang Bin Cheng Hospital of Stomatology Guangdong Provincial Key Laboratory of StomatologyGuanghua School of StomatologySun Yat-sen UniversityGuangzhou 510055China beijing Laboratory of Oral Health Capital Medical UniversityBeijing 100050China Department of Oral Pathology Peking University School and Hospital of Stomatology&National Center of Stomatology&National Clinical Research Center for Oral Diseases&National Engineering Research Center of Oral Biomaterials and Digital Medical DevicesBeijing 100050China Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions Chinese Academy of Medical SciencesBeijing 100050China bgi-Qingdao BGI-ShenzhenQingdao 266555China

The gingiva is a key oral barrier that protects oral tissues from various stimuli.A loss of gingival tissue homeostasis causes periodontitis,one of the most prevalent inflammatory diseases in humans.The human gingiva exists as a complex cell network comprising specialized structures.To understand the tissue-specific pathophysiology of the gingiva,we applied a recently developed spatial enhanced resolution omics-sequencing(Stereo-seq)technique to obtain a spatial transcriptome(ST)atlas of the gingiva in healthy individuals and periodontitis patients.By utilizing Stereo-seq,we identified the major cell types present in the gingiva,which included epithelial cells,fibroblasts,endothelial cells,and immune cells,as well as subgroups of epithelial cells and immune cells.We further observed that inflammation-related signalling pathways,such as the JAK-STAT and NF-κB signalling pathways,were significantly upregulated in the endothelial cells of the gingiva of periodontitis patients compared with those of healthy individuals.Additionally,we characterized the spatial distribution of periodontitis risk genes in the gingiva and found that the expression of IFI16 was significantly increased in endothelial cells of inflamed gingiva.In conclusion,our Stereo-seq findings may facilitate the development of innovative therapeutic strategies for periodontitis by mapping periodontitis-relevant genes and pathways and effector cells.

关键词： spatial transcriptomics gingiva periodontal disease periodontitis risk genes

Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing

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Virologica Sinica 2024年第1期39卷 134-143页

作者： Changcheng Wu Ruhan A Sheng Ye Fei Ye Weibang Huo Roujian Lu Yue Tang Jianwei Yang Xuehong Meng Yun Tang Shuang Chen Li Zhao Baoying Huang Zhongxian Zhang Yuda Chen Dongfang Li Wenling Wang Ke-jia Shan Jian Lu Wenjie Tan NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing100052China Chongqing Municipal Key Laboratory for High Pathogenic Microbes Chongqing Center for Disease Control and PreventionChongqing400042China MGI BGI-ShenzhenShenzhen518083China Thermo Fisher Scientific Beijing100013China School of Public Health Baotou Medical CollegeBaotou014030China bgi PathoGenesis Pharmaceutical Technology Shenzhen518000China State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China College of Life Sciences University of Chinese Academy of SciencesBeijing100049China

The monkeypox virus(MPXV)has triggered a current outbreak globally.Genome sequencing of MPXV and rapid tracing of genetic variants will benefit disease diagnosis and control.It is a significant challenge but necessary to optimize the strategy and application of rapid full-length genome identification and to track variations of MPXV in clinical specimens with low viral loads,as it is one of the DNA viruses with the largest genome and the most AT-biased,and has a significant number of tandem repeats.Here we evaluated the performance of metagenomic and amplicon sequencing techniques,and three sequencing platforms in MPXV genome sequencing based on multiple clinical specimens of five mpox cases in Chinese mainland.We rapidly identified the full-length genome of MPXV with the assembly of accurate tandem repeats in multiple clinical specimens.Amplicon sequencing enables cost-effective and rapid sequencing of clinical specimens to obtain high-quality MPXV genomes.Third-generation sequencing facilitates the assembly of the terminal tandem repeat regions in the monkeypox virus genome and corrects a common misassembly in published sequences.Besides,several intra-host single nucleotide variations were identified in the first imported mpox case.This study offers an evaluation of various strategies aimed at identifying the complete genome of MPXV in clinical specimens.The findings of this study will significantly enhance the surveillance of MPXV.

关键词： Monkeypox virus(MPXV) Metagenomic Next generation sequencing Amplicon Third-generation sequencing

Substrate screening for superclean graphene growth using firstprinciples calculations

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Nano Research 2024年第4期17卷 2216-2222页

作者： Zhihao Li Xiucai Sun Xiaoli Sun Wan-Jian Yin Zhongfan Liu College of Energy Soochow Institute for Energy and Materials InnovationS(SIEMIS)and Jiangsu Provincial Key Laboratory for Advanced Carbon Materials and Wearable Energy TechnologiesSoochow UniversitySuzhou 215006China Graphene Basic Science Research Center Beijing Graphene Institute(BGI)Beijing 100095China Center for Nanochemistry Beijing Science and Engineering Center for NanocarbonsBeijing National Laboratory for Molecular ScienceCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China

Suppressing the formation of amorphous surface carbon and contaminants during the preparation of graphene by chemical vapor deposition remains an ongoing issue.Herein,we analyzed how substrate characteristics affect graphene quality by simulating margin extension,the nucleation process,and defect pegging configurations on mono-crystalline oriented metal substrates with the aim of enhancing graphene cleanliness.Defect formation energy and nucleation potential,which are indirect substrate–graphene interaction features,were found to appropriately evaluate graphene quality.The crystallographic orientation of the metal substrate was discovered to be critical for producing superclean graphene.A low graphene defect density and high nucleation rate on the Cu(100)facet guarantee growth of high-quality graphene,especially in terms of suppressing the formation of amorphous carbon.In addition,rapid kink growth and self-healing on the Cu(100)facet facilitate rapid graphene synthesis,which is also promoted by rapid kink splicing and margin self-repair on this facet.This study provides theoretical insight useful for the synthesis of superclean graphene.

关键词： superclean graphene defects nucleation metal substrates density functional theory calculations

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 species.Assessments of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial sequences.The 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 pressures.Correlation 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 formation.This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.

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

Transfer-free chemical vapor deposition graphene for nitride epitaxy: challenges, current status and future outlook

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Science China Chemistry 2024年第3期67卷 824-840页

作者： Xiang Gao Senlin Li Jingfeng Bi Kaixuan Zhou Meng Li Zhongfan Liu Jingyu Sun College of Energy Soochow Institute for Energy and Materials InnovationsSUDA-BGI Collaborative Innovation CenterKey Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu ProvinceSoochow UniversitySuzhou 215006China beijing Graphene Institute Beijing 100095China Xiamen Silan Advanced Compound Semiconductor Co.Ltd. Xiamen 361026China

Graphene, a two-dimensional material with outstanding electrical and mechanical properties, has attracted considerable attention in the field of semiconductor technologies due to its potential use as a buffer layer for the epitaxial Ⅲ-nitride growth. In recent years, significant progress has been made in the chemical vapor deposition growth of graphene on various insulating substrates for the nitride epitaxy, which offers a facile, inexpensive, and easily scalable methodology. However, certain challenges are still present in the form of producing high-quality graphene and achieving optimal interface compatibility with Ⅲ-nitride materials.In this review, we provide an overview of the bottlenecks associated with the transferred graphene fabrication techniques and the state-of-the-art techniques for the transfer-free graphene growth. The present contribution highlights the current progress in the transfer-free graphene growth on different insulating substrates, including sapphire, quartz, SiO_(2)/Si, and discusses the potential applications of transfer-free graphene in the Ⅲ-nitride epitaxy. Finally, it includes the prospects of the transfer-free graphene growth for the Ⅲ-nitride epitaxy and the challenges that should be overcome to realize its full potential in this field.

关键词： Transfer-free chemical vapor deposition graphene for nitride epitaxy challenges current status and future outlook graphene