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Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of woody Bamboos

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molecular Plant 2019年第10期12卷 1353-1365页

作者： Zhen-Hua Guo Peng-Fei ma Guo-Qian Yang Jin-Yong Hu Yun-Long Liu En-Hua Xia mi-Cai Zhong Lei Zhao Gui-Ling Sun Yu-Xing Xu You-Jie Zhao Yi-Chi Zhang Yu-Xiao Zhang Xue-mei Zhang meng-Yuan Zhou Ying Guo Cen Guo Jing-Xia Liu Xia-Ying Ye Yun-mei Chen Yang Yang Bin Han Choun-Sea Lin Ying Lu De-Zhu Li Germplasm Bank of wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Key Laboratory for Plant Diversity and Biogeography in East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural UniversityHefeiAnhui 230036China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650201China lnstitute of Plant Stress Biology State Key Laboratory of Cotton BiologyDepartment of BiologyHenan UniversityKaifengHenan 475001China College of Big Data and Intelligent Engineering Southwest Forestry UniversityKunmingYunnan 650224China Yunnan Academy of Biodiversity Southwest Forestry UniversityKunmingYunnan 650224China National center for Gene Research Shanghai Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China Agricultural Biotechnology Research center Academia SinicaTaipei College of Fisheries and Life Science Shanghai Ocean UniversityShanghai 201306China

Polyploidization is a major driver of speciation and its importance to plant evolution has been well *** comprise one diploid herbaceous and three polyploid woody lineages,and are members of the only major subfamily in grasses that diversified in forests,with the woody members having a tree-like lignified *** this study,we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels(diploid,tetraploid,and hexaploid).we also constructed a high-density genetic linkage map for a hexaploid species of bamboo,and used a linkage-map-based strategy for genome assembly and identification of subgenomes in *** phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage,and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors.A shared but distinct subgenome was identified in all polyploid forms,and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody *** genetic clues to the unique flowering behavior and woody trait in bamboos were also *** together,our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species,and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

关键词： Bambusoideae polyploidization comparative genomics subgenome evolution flowering

Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox(Pteropus alecto)

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遗传学报:英文版 2023年第8期50卷 554-562页

作者： Haopeng He Hechuan Yang Randy Foo wharton Chan Feng Zhu Yunsong Liu Xuming Zhou Liang ma Lin-Fa wang weiwei Zhai Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Programme in Emerging Infectious Diseases Duke-NUS Medical SchoolSingapore 169857Singapore Singhealth Duke-NUS Global Health Institute Singapore 169857Singapore Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China

As the only mammalian group capable of powered flight,bats have many unique biological *** comparative genomic studies in bats have focused on long-term ***,the microevolutionary processes driving recent evolution are largely *** resequencing data from 50 black flying foxes(Pteropus alecto),one of the model species for bats,we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian *** inference reveals strong population fluctuations(>100 fold)coinciding with multiple historical events including the last glacial change and Toba super eruption,suggesting that the black flying fox is a very resilient species with strong recovery *** long-term adaptation in the black flying fox is enriched in metabolic genes,recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional *** demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary *** together,this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.

关键词： Bats The black flying fox microevolution Population fluctuations Toba eruption

Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage

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genomics, Proteomics & Bioinformatics 2022年第6期20卷 1168-1179页

作者： Yingbo Shen Rong Zhang Dongyan Shao Lu Yang Jiayue Lu Congcong Liu Xueyang wang Junyao Jiang Boxuan wang Congming wu Julian Parkhill Yang wang Timothy R.walsh George F.Gao Zhangqi Shen College of Veterinary medicine China Agricultural UniversityBeijing 100193China Guangdong Laboratory for Lingnan modern Agriculture Guangzhou 510641China CAS Key Laboratory of Pathogenic microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China The Second Affiliated Hospital of Zhejiang University School of medicine Zhejiang UniversityHangzhou 310009China Department of Veterinary medicine University of CambridgeCambridge CB30ESUK Department of Biology University of OxfordOxford OX13SZUK Chinese center for Disease Control and Prevention Beijing 102206China

Emergence of the colistin resistance gene,mcr-1,has attracted worldwide *** the prevalence of mcr-1-positive Escherichia coli(mCRPEC)strains in human carriage showing a significant decrease between 2016 and 2019,genetic differences in mCRPEC strains remain largely *** therefore conducted a comparative genomic study on mCRPEC strains from fecal samples of healthy human subjects in 2016 and *** identified three major differences in mCRPEC strains between these two time ***,the insertion sequence ISApl1 was often deleted and the percentage of mcr-1-carrying IncI2 plasmids was increased in mCRPEC strains in ***,the antibiotic resistance genes(ARGs),aac(3)-IVa and blaCTX-m-1,emerged and coexisted with mcr-1 in ***,mCRPEC strains in 2019 contained more virulence genes,resulting in an increased proportion of extraintestinal pathogenic ***(ExPEC)strains(36.1%)in mCRPEC strains in 2019 compared to that in 2016(10.5%),implying that these strains could occupy intestinal ecological niches by competing with other commensal *** results suggest that despite the significant reduction in the prevalence of mCRPEC strains in humans from 2016 to 2019,mCRPEC exhibits increased resistance to other clinically important ARGs and contains more virulence genes,which may pose a potential public health threat.

关键词： Colistin mcr-1 Escherichia coli genomics Human

Human genetic and immunological determinants of critical COVID-19 pneumonia

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四川生理科学杂志 2021年第11期43卷 1947-1947页

作者： Qian Zhang St Giles Laboratory of Human Genetics of Infectious Diseases Rockefeller Branch The Rockefeller University New York NY USA Laboratory of Human Genetics of Infectious Diseases Necker Branch INSERM U1163 Necker Hospital for Sick Children Paris France University of Paris Imagine Institute Paris France Howard Hughes medical Institute Paris France The Rockefeller University & Howard Hughes medical Institute New York NY USA Necker Hospital for Sick Children & INSERm Paris France Department of Pediatrics Necker Hospital for Sick Children Paris France Cemil Taşcıoglu City Hospital Istanbul Turkey Laboratory of Human Genetics of Infectious Diseases Necker Branch INSERM U1163 Necker Hospital for Sick Children Paris France Imagine Institute University of Paris Paris France Al Jalila Children’s Hospital Dubai United Arab Emirates San Raffaele Telethon Institute for Gene Therapy IRCCS Ospedale San Raffaele and Vita Salute San Raffaele University Milan Italy Hospices Civils de Lyon Lyon France Helix San Mateo CA USA Department of Intensive Care medicine Critical Care Center CHU Lille Lille France Univ. Lille CNRS Inserm CHU Lille Institut Pasteur de Lille U1019-UMR9017-CIIL-Centre d’Infection et d’Immunité deLille Lille France Shupyk National medical Academy for Postgraduate Education Kiev Ukraine Department of medical microbiology University Medical Center Utrecht Utrecht The Netherlands Sidra medicine Doha Qatar Primary Immunodeficiencies Group Department of Microbiology and Parasitology School of Medicine University of Antioquia Medellín Colombia School of microbiology University of Antioquia Medellín Colombia IIBB-CSIC IDIBAPS Barcelona Spain Department of Immunology Second Faculty of Medicine Charles University University Hospital in Motol Prague Czech Republic Department of Immunology Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology Moscow Russia Pulmonology Department Cliniques Universitaire

SARS-CoV-2 infection is benign in most individuals but,in-10%of cases,it triggers hypoxemic COVID-19 pneumonia,which becomes critical in-3%of *** ensuing risk of death(-1%)doubles every five years from childhood onward and is-1.5 times greater in men than in *** are the molecular and cellular determinants of critical COVID-19 pneumonia?Inborn errors of type I IFNs,including autosomal TLR3 and X-linked TLR7 deficiencies,are found in-1-5%of patients with critical pneumonia under 60 years old.

关键词： pneumonia critical cases

monsoon boosted radiation of the endemic East Asian carps

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Science China(Life Sciences) 2023年第3期66卷 563-578页

作者： Chenguang Feng Kun wang wenjie Xu Liandong Yang Kunyuan wanghe Ning Sun Baosheng wu Feixiang wu Lei Yang Qiang Qiu Xiaoni Gan Yiyu Chen Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China School of Ecology and Environment Northwestern Polytechnical UniversityXi'an 710072China Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences Northwest Institute of Plateau BiologyChinese Academy of SciencesXining 810008China University of Chinese Academy of Sciences Beijing 100039China Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China Florida museum of Natural History University of FloridaGainesvilleFL 32611USA National Natural Science Foundation of China Beijing 100085China center for Excellence in Animal Evolution and Genetics Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China

major historical events often trigger the rapid flourishing of a few lineages,which in turn shape established biodiversity *** did this process occur and develop?This study provides a window into this *** endemic East Asian carps(EEAC)dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems.A series of evidence,including ecogeography,phylogenetics,and macroevolution,suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon *** further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting(e.g.,marine transgression and regression and glacial-interglacial cycle)have further reshaped the distribution patterns of EEAC’s *** genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting,which boosted ***,this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.

关键词： adaptive radiation Xenocyprididae east Asian monsoon genomes macroevolution phylogenomics

Comprehe nsive an alysis of SSRs and database construction using all complete gene-cod ing sequences in major horticultural and represe ntative plants

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Horticulture Research 2021年第1期8卷 1766-1782页

作者： Xiaoming Song Qihang Yang Yun Bai Ke Gong Tong wu Tong Yu Qiaoying Pei weike Duan Zhinan Huang Zhiyuan wang Zhuo Liu Xi Kang wei Zhao Xiao ma School of Life Sciences/Library North China University of Science and TechnologyTangshanHebei 063210China School of Life Science and Technology and center for Informational Biology University of Fleetronic Science and Technology of China610054 ChengduChina Food Science and Technology Department University of Nebraska-LincolnLincolnNE 68588USA College of Life Sciences and Food Engineering Huaiyin In stitute of Technology223003 Huai'anChina

Simple sequence repeats(SSRs)are one of the most important genetic markers and widely exist in most ***,we identified 249,822 SSRs from 3,951,919 genes in 112 ***,we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database(PSSRD).Interestingly,more SSRs were found in lower plants than in higher plants,showing that lower plants needed to adapt to early extreme *** specific enriched functional terms in the lower plant Chlam^tdomonas reinhardtii were detected when it was compared with seven other higher *** addition,Guanylate_cyc existed in more genes of lower plants than of higher *** our PSSRD,we constructed an interactive plotting function in the chart interface,and users can easily view the detailed information of *** SSR information,including sequences,primers,and annotations,can be downloaded from our ***,we developed web SSR Finder and Batch SSR Finder tools,which can be easily used for identifying *** database was developed using PHP,HTmL,J avaScript,and mySQL,which are freely available at http://***/.we conducted an analysis of the myb gene families and flowering genes as two applications of the *** analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the myb gene *** SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

关键词： PHP HTmL web

Comprehensive identification and characterization of simple sequence repeats based on the whole-genome sequences of 14 forest and fruit trees

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Forestry Research 2021年第1期1卷 56-65页

作者： Xiaoming Song Nan Li Yuanyuan Guo Yun Bai Tong wu Tong Yu Shuyan Feng Yu Zhang Zhiyuan wang Zhuo Liu Hao Lin School of Life Science and Technology and center for Informational Biology University of Electronic Science and Technology of ChinaChengdu 610054China School of Life Sciences/School of Economics North China University of Science and TechnologyTangshanHebei 063210China Food Science and Technology Department University of Nebraska-LincolnLincolnNE 68588USA

Simple sequence repeats(SSRs)are popular and important molecular markers that exist widely in ***,we conducted a comprehensive identification and comparative analysis of SSRs in 14 tree species.A total of 16,298 SSRs were identified from 429,449 genes,and primers were successfully designed for 99.44% of the identified *** analysis indicated that tri-nucleotide SSRs were the most abundant,with an average of~834 per *** enrichment analysis by combining SSR-containing genes in all species,revealed 50 significantly enriched terms,with most belonging to transcription factor families associated with plant development and abiotic stresses such as myeloblastosis_DNA-bind_4(myb_DNA-bind_4),APETALA2(AP2),and Fantastic Four meristem regulator(FAF).Further functional enrichment analysis showed that 48 terms related to abiotic stress regulation and floral development were significantly enriched in ten species,whereas no significantly enriched terms were found in four ***,the largest number of enriched terms was detected in Citrus sinensis(L.)Osbeck,accounting for 54.17% of all significantly enriched functional ***,we analyzed AP2 and trihelix gene families(myb_DNA-bind_4)due to their significant enrichment in SSR-containing *** results indicated that whole-genome duplication(wGD)and whole genome triplication(wGT)might have played major roles in the expansion of the AP2 gene family but only slightly affected the expansion of the trihelix gene family during *** conclusion,the identification and comprehensive characterization of SSR markers will greatly facilitate future comparative genomics and functional genomics studies.

关键词： species enriched characterization

The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

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Fungal Diversity 2021年第4期109卷 27-55页

作者： Teun Boekhout m.Catherine Aime Dominik Begerow Toni Gabaldón Joseph Heitman martin Kemler Kantarawee Khayhan marc-AndréLachance Edward J.Louis Sheng Sun Duong Vu Andrey Yurkov westerdijk Fungal Biodiversity Institute UtrechtThe Netherlands Institute of Biodiversity and Ecosystem Dynamics(IBED) University of AmsterdamAmsterdamThe Netherlands Dept Botany and Plant Pathology College of AgriculturePurdue UniversityWest LafayetteIN 47907USA Evolution of Plants and Fungi Ruhr-University Bochum44801 BochumGermany Barcelona Supercomputing Centre(BSC-CNS) Jordi Girona2908034 BarcelonaSpain Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and TechnologyBaldiri Reixac1008028 BarcelonaSpain Catalan Institution for Research and Advanced Studies(ICREA) BarcelonaSpain Department of molecular Genetics and microbiology Duke University Medical CenterDurhamNC 27710USA Department of microbiology and Parasitology Faculty of Medical SciencesUniversity of PhayaoPhayao 56000Thailand Department of Biology University of Western OntarioLondonON N6A 5B7Canada Department of Genetics and Genome Biology Genetic Architecture of Complex TraitsUniversity of LeicesterLeicester LE17RHUK German Collection of microorganisms and Cell Cultures Leibniz Institute DSMZBrunswickGermany

Here we review how evolving species concepts have been applied to understand yeast ***,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth *** the biological species concept was added,which applied data from mating *** measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal *** present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence *** application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic *** genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they *** seems a relatively common phenomenon and has been observed in all major fungal lineages that contain *** that hybrids may greatly differ in their post-hybridization *** in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.

关键词： Fungi Species concepts comparative genomics Hybrids Nomenclature Taxonomy

Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health

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Infectious Diseases of Poverty 2023年第6期12卷 34-50页

作者： minyu Zhou Lian Xu Dahua Xu wen Chen Jehangir Khan Yue Hu Hui Huang Hang wei Yiqing Zhang Phiraphol Chusongsang Kanthi Tanasarnprasert Xiang Hu Yanin Limpanont Zhiyue Lv Key Laboratory of Tropical Disease Control Ministry of EducationSun Yat-Sen UniversityGuangzhouChina Department of Pathogen Biology and Biosafety Zhongshan School of MedicineSun Yat-Sen UniversityGuangzhouChina Key Laboratory of Neuroregeneration Ministry of Education and Jiangsu ProvinceCo-Innovation Center of NeuroregenerationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsNantong UniversityNantongChina Key Laboratory of Tropical Translational medicine of ministry of Education College of Biomedical Information and EngineeringHainan Medical UniversityHaikouChina Key Laboratory of Vascular Biology and Translational medicine Medical SchoolHunan University of Chinese MedicineChangshaChina Hainan General Hospital Hainan Afliated Hospital of Hainan Medical UniversityHaikouChina Department of Social and Environmental medicine Faculty of Tropical MedicineMahidol UniversityBangkokThailand State Key Laboratory of Developmental Biology of Freshwater Fish College of Life SciencesHunan Normal UniversityChangshaChina.

Background Schistosoma mekongi is a human blood fluke causing schistosomiasis that threatens approximately 1.5 million humans in the world. Nonetheless, the limited availableS. mekongi genomic resources have hindered understanding of its biology and parasite-host interactions for disease management and pathogen control. The aim of our study was to integrate multiple technologies to construct a high-quality chromosome-level assembly of theS. mekongi *** The reference genome forS. mekongi was generated through integrating Illumina, PacBio sequencing, 10 × genomics linked-read sequencing, and high-throughput chromosome conformation capture (Hi-C) methods. In this study, we conducted de novo assembly, alignment, and gene prediction to assemble and annotate the genome. comparative genomics allowed us to compare genomes across different species, shedding light on conserved regions and evolutionary relationships. Additionally, our transcriptomic analysis focused on genes associated with parasite-snail interactions inS. mekongi infection. we employed gene ontology (GO) enrichment analysis for functional annotation of these *** In the present study, theS. mekongi genome was both assembled into 8 pseudochromosomes with a length of 404 mb, with contig N50 and scaffold N50 lengths of 1168 kb and 46,759 kb, respectively. we detected that 43% of the genome consists of repeat sequences and predicted 9103 protein-coding genes. we also focused on proteases, particularly leishmanolysin-like metalloproteases (m8), which are crucial in the invasion of hosts by 12 flatworm species. Through phylogenetic analysis, it was discovered that the m8 gene exhibits lineage-specific amplification among the genusSchistosoma. Lineage-specific expansion of m8 was observed in blood flukes. Additionally, the results of the RNA-seq revealed that a mass of genes related to metabolic and biosynthetic processes were upregulated, which might be beneficial for cercaria ***

关键词： Schistosoma mekongi Chromosome-scale genome Protease RNA-seq