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A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and droughttolerance mechanisms

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Plant Communications 2024年第7期5卷 157-177页

作者： Lei Feng Fei Teng Na Li Jia-Cheng Zhang Bian-Jiang Zhang Sau-Na Tsai Xiu-Le Yue Li-Fei Gu Guang-Hua Meng Tian-Quan Deng Suk-Wah Tong Chun-Ming Wang Yan Li Wei Shi Yong-Lun Zeng Yue-Ming Jiang Weichang Yu Sai-Ming Ngai Li-Zhe An Hon-Ming Lam Jun-Xian He School of Life Sciences and State Key Laboratory of Agrobiotechnology The Chinese University of Hong KongSha TinNew TerritoriesHong KongChina Guangdong Provincial Key Laboratory of Biotechnology for Plant Development School of Life SciencesSouth China Normal UniversityGuangzhou 510631China bgi-Shenzhen Tech Co. Ltd.Beishan Industrial ZoneYantian DistrictShenzhen 518083China School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations Lanzhou UniversityLanzhou 730030China State Key Laboratory of Subtropical Silviculture Zhejiang Agriculture and Forestry UniversityHangzhou 311300China State Key Laboratory of Plant Diversity and Specialty Crops South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China Guangdong Provincial Key Laboratory of Applied Botany&Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China college of Life Sciences and Oceanography Shenzhen UniversityShenzhen 518060China State Key Laboratory of Efficient Production of Forest Resources Beijing Forestry UniversityBeijing 100083China

Plants that grow in extreme environments represent unique sources of stress-resistance genes and *** mongolicus(Leguminosae)is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions;however,its drought-tolerance mechanisms remain poorly ***,we report the assembly of a reference-grade genome for ***,describe its evolutionary history within the legume family,and examine its drought-tolerance *** assembled genome is 843.07 Mb in length,with 98.7%of the sequences successfully anchored to the nine chromosomes of *** genome is predicted to contain 47611 protein-coding genes,and 70.71%of the genome is composed of repetitive sequences;these are dominated by transposable elements,particularly longterminal-repeat *** analyses revealed two whole-genome duplication(WGD)events at 130 and 58 million years ago(mya)that are shared by the genus Ammopiptanthus and other legumes,but no species-specific WGDs were found within this *** genome reconstruction revealed that the *** genome has undergone fewer rearrangements than other genomes in the legume family,confirming its status as a"relict plant".Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed,both under normal conditions and in response to polyethylene glycol-induced *** induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress,suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in *** expression of AmERF2,an ethylene response factor unique to ***,can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants,demonstrating the potential for application of *** genes in crop improvement.

关键词： Ammopiptanthus mongolicus genome sequencing genome evolution drought tolerance cuticular wax ethylene

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Graphene: A promising candidate for charge regulation in high-performance lithium-ion batteries

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Nano Research 2021年第12期14卷 4370-4385页

作者： Danping Sun Zhi Tan Xuzheng Tian Fei Ke Yale Wu Jin Zhang college of Chemistry and Molecular Engineering Beijing Science and Engineering Center for NanocarbonsBeijing National Laboratory for Molecular SciencesPeking UniversityBeijing100871China Beijing Graphene Institute(bgi) Beijing100095China

The development of rechargeable lithium-ion batteries (LIBs) is being driven by the ever-increasing demand for high energy density and excellent rate performance. Charge transfer kinetics and polarization theory, considered as basic principles for charge regulation in the LIBs, indicate that the rapid transfer of both electrons and ions is vital to the electrochemical reaction process. Graphene, a promising candidate for charge regulation in high-performance LIBs, has received extensive investigations due to its excellent carrier mobility, large specific surface area and structure tunability, etc. Recent progresses on the structural design and interfacial modification of graphene to regulate the charge transport in LIBs have been summarized. Besides, the structure-performance relationships between the structure of the graphene and its dedicated applications for LIBs have also been clarified in detail. Taking graphene as a typical example to explore the mechanism of charge regulation will outline ways to further understand and improve carbon-based nanomaterials towards the next generation of electrochemical energy storage devices.

关键词： graphene charge transport lithium-ion battery electron and ion transfer

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Screening for viruses in lung adenocarcinoma in China

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Chinese Medical Journal Pulmonary and Critical Care Medicine 2024年第3期2卷 197-199页

作者： Zhuxing Chen Peng Liang Haoxiang Xu Shengli Yang Jilong Liu Shifu Chen Ran Zhong Akira Sugimoto Wenhua Liang Jianxing He Tomoya Kawaguchi Department of Thoracic Surgery and Oncology the First Affiliated Hospital of Guangzhou Medical UniversityChina State Key Laboratory of Respiratory Disease&National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdong 510120China Pulmonary Nodule Surgical Department the First People’s Hospital of FoshanFoshanGuangdong 528000China Center for Medical Research the First People’s Hospital of YulinThe Sixth Affiliated Hospital of Guangxi Medical UniversityYulinGuangxi 537000China Department of General Medicine the Second Affiliated Hospital(Guangdong Provincial Hospital of Chinese Medicine)Guangzhou University of Chinese MedicineGuangzhouGuangdong 510120China Day Surgery Center the First People’s Hospital of FoshanFoshanGuangdong 528000China bgi Genomics BGI-ShenzhenShenzhenGuangdong 510120China HaploX Biotechnology Co.LtdShenzhenGuangdong 518000China Department of Respiratory Medicine Graduate School of MedicineOsaka Metropolitan UniversityChemotherapy CenterOsaka City University HospitalOsaka 558-8585Japan The First Clinical college Southern Medical UniversityGuangzhouGuangdong 510120China

To the Editor,Considerable numbers of cases of lung adenocarcinoma(LUAD)in non-smokers with unclear etiology have been *** and bacterial infections are the common causes of lung and respiratory diseases.1 However,whether LUAD development coexists with virus infection is still *** staining and polymerase chain reaction(PCR)are often used to detect virus in blood,sputum,and alveolar lavage fluid ***-genome sequencing(WGS)is an unbiased method with a high throughput nature that can be applied for a broader assessment of *** studies described the viral landscape in pan-cancer in The Cancer Genome Atlas(TCGA)or cohort studies;however,these studies did not include Asian ***,we sought to screen the common viral pathogens in a nationwide cohort of LUAD patients in China and further explored other potential viral pathogens by analyzing the WGS data from our single-center cohort.2 To systematically investigate the viral associations with LUAD in China,we conducted a comprehensive study that included two distinct cohorts.

关键词： adenocarcinoma lung respiratory

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Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows

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National Science Review 2020年第1期7卷 113-127页

作者： Yanhua Qu Chunhai Chen Ying Xiong Huishang She Yong E Zhang Yalin Cheng Shane Du Bay Dongming Li Per G P Ericson Yan Hao Hongyuan Wang Hongfeng Zhao Gang Song Hailin Zhang Ting Yang Chi Zhang Liping Liang Tianyu Wu Jinyang Zhao Qiang Gao Weiwei Zhai Fumin Lei Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences bgi Genomics BGI-Shenzhen University of Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Committee on Evolutionary Biology University of Chicago Life Sciences Section Integrative Research Center Field Museum of Natural History Key Laboratory of Animal Physiology Biochemistry and Molecular Biology of Hebei Province College of Life Sciences Hebei Normal University Department of Bioinformatics and Genetics Swedish Museum of Natural History college of Life Sciences Shaanxi Normal University China National Gene Bank BGI-Shenzhen Human Genetics Genome Institute of Singapore Agency for Science Technology and Research

Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.

关键词： denovo genome early stage adaptation high elevation muscle phenotypes polygenic adaptation regulatory evolution

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China is initiating the Aquatic 10-100-1,000 Genomics Program

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Science China(Life Sciences) 2017年第3期60卷 329-332页

作者： Yingjie Liu Pao Xu Junmin Xu Yu Huang Yongxin Liu Hui Fang Yinchang Hu Xinxin You Chao Bian Min Sun Ruobo Gu Lifeng Cui Xianliang Zhang Peng Xu Qiong Shi Chinese Academy of Fishery Sciences Beijing 100141 China bgi Research Center for Aquatic Genomics Chinese Academy of Fishery Sciences Shenzhen 518083 China Freshwater Fisheries Research Center Chinese Academy of Fishery Sciences Wuxi 214081 China bgi Shenzhen Academy of Marine Sciences BGI Fisheries BGI Shenzhen 518083 China Pearl River Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou 510380 China Marine Research Center College of Life Sciences and Oceanography Shenzhen University Shenzhen 518060 China

On June 17 of 2016,a group of scientists from Chinese Academy of Fishery Sciences（CAFS）and Shenzhen bgi Fisheries Sci＆Tech ***.（bgi Fisheries）met together in Shenzhen,China to launch a novel project,the China Aquatic 10-100-1,000 Genomics Program,to conduct molecular breeding of-10 aquaculture species and sequence genomes of-100 and transcriptomes of-1,000 aquatic species.

关键词：中国水产科学研究院基因组计划水产科技基因组序列 CAFS 分子育种 bgi 科学家

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Whole-genome resequencing of Japanese whiting(Sillago japonica) provide insights into local adaptations

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Zoological Research 2021年第5期42卷 548-561页

作者： Zhi-Qiang Han Xin-Yu Guo Qun Liu Shan-Shan Liu Zhi-Xin Zhang Shi-Jun Xiao Tian-Xiang Gao Fishery college Zhejiang Ocean UniversityZhoushanZhejiang 316002China bgi-Qingdao BGI-ShenzhennQingdaoShandong 266555China Graduate School of Marine Science and Technology Tokyo University of Marine Science and TechnologyKonanMinatoTokyo 108-8477Japan Institute of Fisheries Science Tibet Academy of Agricultural and Animal Husbandry SciencesLhasaTibet 850000China

The genetic adaptations of various organisms to heterogeneous environments in the northwestern Pacific remain poorly *** genomic divergence among populations may reflect *** understanding of the mechanisms by which organisms adapt to different temperatures in response to climate change and predicting the adaptive potential and ecological consequences of anthropogenic global warming are *** sequenced the whole genomes of Japanese whiting(Sillago japonica)specimens collected from different latitudinal locations along the coastal waters of China and Japan to detect possible thermal *** population genomics,a total of 5.48 million single nucleotide polymorphisms(SNPs)from five populations revealed a complete genetic break between the Chinese and Japanese groups,which was attributed to both geographic distance and local *** shared natural selection genes between two isolated populations(i.e.,Zhoushan and Ise Bay/Tokyo Bay)indicated possible parallel evolution at the genetic level induced by *** genes also indicated that the process of temperature selection on isolated populations is ***,we observed natural candidate genes related to membrane fluidity,possibly underlying adaptation to cold environmental *** findings advance our understanding of the genetic mechanisms underlying the rapid adaptations of fish *** distribution projection models suggested that the Chinese and Japanese groups may have different responses to future climate change,with the former expanding and the latter *** findings of this study enhance our understanding of genetic differentiation and adaptation to changing environments.

关键词： Sillago japonica Local adaptation Climate change Temperature stress Wholegenome resequencing

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High-quality chromosome-level genome assembly of redlip mullet(Planiliza haematocheila)

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Zoological Research 2021年第6期42卷 796-799页

作者： Na Zhao Hao-Bing Guo Lei Jia Qiu-Xia Deng Chun-Hua Zhu Bo Zhang Southern Marine Science and Engineering Guangdong Laboratory(Zhanjiang) Fisheries CollegeGuangdong Ocean UniversityZhanjiangGuangdong 524088China Tianjin Fisheries Research Institute Tianjin 300200China Shanghai Ocean University Shanghai 201306China bgi-Qingdao BGI-ShenzhenQingdaoShandong 266555China

In the present study,we successfully assembled a high-quality genome of Planiliza haematocheila(redlip mullet)based on Oxford Nanopore long read,single-tube long fragment read(stLFR),and Hi-C chromatin interaction *** size of the *** genome was 652.91 *** than 93.8%of BUSCO genes were detected,and the N50 lengths of contigs and scaffolds reached 7.21 Mb and 28.01 Mb,respectively,thus demonstrating outstanding genome completeness and sequence continuity.A total of 21045 protein-coding genes were predicted in the assembled genome,and 99.77%of those genes were functionally *** genomic and phylogenetic analyses revealed the adaptability of *** to complex living environments at the genomic level,highlighting its broad adaptability and resistance to multiple stresses as an important economic *** high-quality reference chromosome-level genome of *** provides a powerful genomic resource for further systematic study of Mugilidae.

关键词： environments quality adaptability

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Long-read sequencing(method of the year 2022):The way forward for plant omics research

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Molecular Plant 2023年第5期16卷 791-793页

作者： Sunil Kumar Sahu Huan Liu State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China college of Life Sciences University of Chinese Academy of SciencesBejing 100049China

Long-read sequencing(LRS)technology along with the recent development of computational tools,crowned the“method of the year 2022”(Marx,2023),have made it possible to sequence and assemble the genomes of practically every representative species(Kovaka et al.,2023).By considering its immense role and potential in advancing scientific research,the LRS market was valued at$1.35 billion in 2021 and is anticipated to reach$4.4 billion by 2031,growing at a compound annual growth rate of 14.4%from 2022 to 2031(***).Here,we discuss the current state and advantages of LRS technologies,the successful cases and novel discoveries with LRS,potential broad applications in plant genomics research,and the challenges that still need to be overcome in the future.

关键词： overcome crown method

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A genetic solution for the global food security crisis

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Journal of Integrative Plant Biology 2023年第6期65卷 1359-1361页

作者： Sunil K.Sahu Huan Liu State Key Laboratory of Agricultural Genomics BGI‐ShenzhenShenzhen518083China college of Life Sciences University of Chinese Academy of SciencesBeijing100049China

Due to the rapid increase in population and the decreasing availability of arable land and freshwater resources per capita,global crop production will need to double by 2050 to meet human food *** early March,the World Bank and the Food and Agriculture Organization(FAO)of the United Nations released a report saying that 45 countries are in urgent need of food aid and millions of people are in severe hunger(https://***/en/topic/agriculture/brief/food-security-update).

关键词： global security urgent

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Emerging Two‑dimensional Materials Constructed Nanofuidic Fiber:Properties,Preparation and Applications

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Advanced Fiber Materials 2022年第2期4卷 129-144页

作者： Shuo Li Yaogang Li Yuanlong Shao Hongzhi Wang Key Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu Province College of EnergySUDA-BGI Collaborative Innovation CenterSoochow Institute for Energy and Materials Innovations(SIEMIS)Soochow UniversitySuzhou 215006People’s Republic of China State Key Laboratory for Modifcation of Chemical Fibers and Polymer Materials College of Materials Science and EngineeringDonghua University ShanghaiShanghai 201620People’s Republic of China Beijing Graphene Institute(bgi) Beijing 100095People’s Republic of China

By virtue of ultra-fexibility and non-inductive feature,fbrous electrode is an ideal platform for constructing wearable electronics and implantable electrodes for medical therapy.2D nanofuidic channels with tailored ion transport dynamics enable minimized charge transfer resistance and efcient ion transport ***,combining the nanofuidic ion transport features and fbrous electrode advantages,2D nanofuidic fber electrode presents a series of extra advantages of unidirectional efcient ion transport and great *** this minireview,we frst elaborate the architecture characteristics of the emerging 2D nanofuidic fbers and highlight the intriguing features,such as tunable interlayer spacing,efcient ion transport and modifable channel *** strategies for constructing 2D nanofuidic fbers have been systematically enumerated,including solvent volatilizing regulation,confnement triggered alignment,and fow-driven *** addition,the promising applications of 2D nanofuidic fbers have been also summarized as ***,we analyze the challenges and perspectives of fbrous 2D nanofuidic construction,ion transport mechanism study and potential application extension.

关键词： Two-dimensional nanofuidic fber Nanofuidic channel Ion transport

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