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complete genome sequence of Clostridium carboxidivorans P7T,a syngas-fermenting bacterium capable of producing long-chain alcohols

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Complete genome sequence of Clostridium carboxidivorans P7T,...

Analysis on complete genome sequence of Japanese Encephalitis Inactivated Vaccine Seed Strain

2015中国遗传学会大会

作者： Ning Li Junjie Yang Changsheng Chai Weihong Jiang Yang Gu Key Laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of Sciences University of Chinese Academy of Sciences

Biological use of synthesis gas(syngas)derived from a variety of carbon-contained materials,***,coal,municipal refuse and plant off-gases,to produce chemicals has good application prospects,and has attracted increasing interests in recent years(Wilkins and Atiyeh,2011;Fast et al.,2015).*** P7T(ATCC BAA-624 and DSM 15243)can autotrophically grow with syngas by using CO or CO2 and H2 ***,this Clostridium strain is one of the few microorganisms capable of producing long-chain alcohols(*** and hexanol)besides ethanol(Phillips et al.,2015;Ramio-Pujol et al.,2015).The draft genome sequence of *** P7T has been successively presented by using the 454 Life Sciences genome sequencer FLX system(Bruant et al.,2010;Hemme et al.,2010;Paul et al.,2010).The sequence data showed a circular chromosome and a mega-plasmid in ***,until now,the complete genome sequence of P7T has not been obtained,which may be due to problems occurred during the assembling *** this study,*** P7T(DSM-15243)was resequenced by using the PacBio RS II system,which enabled us to establish the complete genome *** following de novo assembly was finished by using SPAdes 3.5.0(Bankevich et al.,2012).Annotation of the genome was finished with the NCBI Prokaryotic genome Annotation Pipeline(PGAP).The sequencing result finally determined a 5,752,782 bp genome(including a19,902 bp mega-plasmid)that comprises 4,973 coding *** genome version is 82,083 bp larger than that from the lasted draft genome sequence(Bruant et al.,2010).genome features of *** P7T are summarized(Table 1).In sum,in this study,use of the PacBio RS II system sequencing method finally provides a complete genome of *** *** new genome sequence paves ways for further comparative transcdptomic analysis of P7T,which could be valuable for genetic modification of this anaerobe for more efficient syngas utilization and che

关键词： Clostridium carboxidivorans complete genome sequence

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Analysis on Complete Genome Sequence of Japanese Encephaliti...

A Comparison of complete genome sequences of a Rabies Virus Chinese Isolate SH06 with the Vaccine Strains

2013年中国药学大会暨第十三届中国药师周

作者： Xinyu Liu Yongxin Yu Hongshan Xu Guangzhi Yue Lihong Yang Guanmu Dong Yuhua Li Lili Jia Division of Arboviral Vaccine Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products National Institute for Food and Drug Control

Japanese encephalitis （JE） is the main cause of viral encephalitis in many countries of Asia. The infection is mosquito-borne and caused by the JE virus. The control of JE is based essentially by immunization. JE inactivated vaccine derived from JEV P3 strain （P3-Smb53） have been available in China since decades and have proved effective to control the disease. But the molecular characteristics of the vaccine seed have not been elucidated. In our study, we determined the complete genome sequence and compared with all JEV sequences in GenBank. The results from this study demonstrated that the vaccine seed is 10,976 nucleotides in length and has the same organization as most JEV strains. Even though there are some differences on nucleotide and amino acid sequence among P3-Smb53 and other JEV strains, but on the 12 critical neutralizing epitopes confirmed previously, all the isolates are highly consistent with P3-Smb53. So we conclude that JE inactivated vaccine derived from P3-Smb53 could protect against all the present isolates in nature.

关键词： Japanese encephalitis Inactivated vaccine seed complete genome sequence

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Virologica Sinica 2009年第6期24卷 529-536页

作者： Sheng-li MENG Ge-Lin XU Jie WU Xiao-Ming YANG Jia-Xin YAN Center of Rabies Diagnosis Wuhan Institute of Biological Products Wuhan 430060 China

In this study, we determined the complete nucleotide and deduced amino acid sequence of a primary isolate of rabies virus (SH06) obtained from the brain of a rabid dog. The overall length of the genome was 11 924 nucleotides. Comparison of the genomic sequence showed the homology of SH06 at nucleotide level with full-length genomes of reference vaccine strains ranged from 82.2% with the PV strain to 86.9% with the CTN strain. A full-length genome-based phylogenetic analysis was performed with sequences available from GenBank. Phylogenetic analysis of the complete genome sequences indicated that the SH06 exhibited the highest homology with rabies street virus BD06 and CTN vaccine strain originated from China.

关键词： Rabies virus complete genome sequence Phylogenetic analysis

Molecular analysis of Coxsackievirus A24 variant isolates from three outbreaks of acute hemorrhagic conjunctivitis in 1988,1994 and 2007 in Beijing,China

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Virologica Sinica 2022年第2期37卷 168-176页

作者： Junhan Li Fang Huang Yong Zhang Tianjiao Ji Shuangli Zhu Dongyan Wang Zhenzhi Han Jinbo Xiao Fenfen Si Wenbo Xu Dongmei Yan National Polio Laboratory WHO WPRO Regional Polio Reference LaboratoryNational Health Commission Key Laboratory for BiosecurityNational Health Commission Key Laboratory for Medical VirologyNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing102206China Nanguan District Center for Disease Control and Prevention Changchun130042China Beijing Center for Disease Control and Prevention Beijing100000China Center for Biosafety Mega-Science Chinese Academy of SciencesWuhan430000China

Coxsackievirus A24 variant(CVA24v)is a major pathogen that causes continued outbreaks and pandemics of acute hemorrhagic conjunctivitis(AHC).In China,the first confirmed outbreak of CVA24v-related AHC occurred in Beijing in 1988,followed by another two significant outbreaks respectively in 1994 and 2007,which coincides with the three-stage dynamic distribution of AHC in the world after *** illustrate the genetic characteristics of CVA24v in different periods,a total of 23 strains were isolated from those three outbreaks and the whole genome of those isolations were sequenced and *** with the prototype strain,the 23 strains shared four nucleotide deletions in the 5'UTR except the 0744 strain isolated in *** at the 98th site,one nucleotide insertion was found in all the strains collected from *** 1994 to 2007,amino acid polarity in the VP1 region at the 25th and the 32nd site were *** the 3C and VP1 phylogenetic tree indicated that isolates from 1988 and 1994 belonged to Genotype III(GIII),and 2007 strains to Genotype IV(GIV).According to the Bayesian analysis based on complete genome sequence,the most recent common ancestors for the isolates in1988,1994 and 2007 were respectively estimated around October 1987,February 1993 and December *** evolutionary rate of the CVA24v was estimated to be 7.45×10^(-3) substitutions/site/*** study indicated that the early epidemic of CVA24v in Chinese mainland was the *** mutations and amino acid changes in different genotypes of CVA24v may generate intensity differences of the AHC ***24v has been evolving constantly with a relatively rapid rate.

关键词： Coxsackievirus A24 variant(CVA24v) Acute hemorrhagic conjunctivitis(AHC) Phylogenetic analysis complete genome sequence

complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae

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Journal of Oceanology and Limnology 2018年第2期36卷 528-536页

作者： TANG Xianghai XU Kuipeng HAN Xiaojuan MO Zhaolan MAO Yunxiang Ministry of Education Key Laboratory of Marine Genetics and Breeding College of Marine Life Sciences Ocean University of China Qingdao 266003 China Key Laboratory of Sustainable Development of Marine Fisheries Ministry of Agriculture Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Qingdao 266071 China CAS Key Laboratory of Biobased Materials Qingdao Institute of Bioenergy and Bioproeess Technology Chinese Academy of Sciences Qingdao 266101 China

Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022T using single molecule real-time sequencing technology （SMRT） and performed comparative genomics and phylogenomics analyses. The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 tRNA genes, and 21 rRNA genes. The C. marina JCM 2102U genome contained a set of crucial genes involved in surface colonization processes. The comparative genome analysis indicated the significant differences between C. marina JCM 21022T and Cobetia amphilecti KMM 296 （formerly named C. marina KMM 296） resulted from sequence insertions or deletions and chromosomal recombination. Despite these differences, pan and core genome analysis showed similar gene functions between the two strains. The phylogenomic study of the family Halomonadaceae is relationships were well resolved among every genera Cobetia, Kushneria, Zymobacter, and Halotalea. reported here for the first time. We found that the tested, including Chromohalobacter, Halomonas,

关键词： Cobetia marina JCM 21022r Halomonadaceae complete genome sequence comparativegenomics phylogenomics surface colonization single molecule real-time sequencingtechnology (SMRT)

A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus

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Synthetic and Systems Biotechnology 2016年第3期1卷 169-186页

作者： Biao Tang Feng Xie Wei Zhao Jian Wang Shengwang Dai Huajun Zheng Xiaoming Ding Xufeng Cen Haican Liu Yucong Yu Haokui Zhou Yan Zhou Lixin Zhang Michael Goodfellow Guo-Ping Zhao State Key Laboratory of Genetic Engineering Department of MicrobiologySchool of Life Sciences and Institute of Biomedical SciencesFudan UniversityShanghai200438China CAS-Key Laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China CAS-Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesNo.1 Beichen West RoadChaoyang DistrictBeijing100101China Shanghai-MOST Key Laboratory of Disease and Health Genomics Chinese National Human Genome Center at ShanghaiShanghai201203China State Key Laboratory for Infectious Diseases Prevention and Control Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesNational Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina Department of Microbiology and Li Ka Shing Institute of Health Sciences The Chinese University of Hong KongPrince of Wales HospitalShatinNew TerritoriesHong Kong SARChina School of Biology University of NewcastleNewcastle upon TyneNE17RUUK

The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239T was generated,revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences(CDSs).Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17T,Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures,including various genome sizes,core/quasi-core/non-core configurations and different kinds of *** polyketide synthase gene clusters were absent from the *** genome,12 gene clusters related to the biosynthesis of other specialized(secondary)metabolites were *** pathways attributable to the facultative methylotrophic physiology of *** strain 239T,including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle,were identified together with evidence that the latter might be the result of horizontal gene *** analyses based on 16S rDNA or orthologues of AMETH_3452,a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains,respectively,revealed three major phyletic lineages,namely the mesophilic or moderately thermophilic *** subclade(AOS),the mesophilic Amycolatopsis taiwanensis subclade(ATS)and the thermophilic *** subclade(AMS).The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible *** study shows the value of integrating conventional taxonomic with whole genome sequence data.

关键词： Amycolatopsis methanolica complete genome sequence One carbon metabolism Sub-generic phyletic clades AOS ATS AMS

Genetic characterizations and molecular epidemiology of human echovirus 30 isolated from Ningxia,China

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Biosafety and Health 2023年第6期5卷 346-354页

作者： Fang Yuan Xinfeng Wei Xueping Ma Jiangtao Ma Xuemin Ma Xiaoqiang Sun Min Cao Juan Zhou Wei Zhang Hui Chen Rui Wang Jichen Li Qiang Sun Ningxia Hui Autonomous Region Center for Disease Control and Prevention Yinchuan 750004China Ningxia Hui Autonomous Region People's Hospital Yinchuan 750021China National Laboratory for Poliomyelitis WHO WPRO Regional Polio Reference LaboratoryNational Key Laboratory for TraceabilityEarly Warning and Intlligent Decision of Infectious DiseasesNational Health Commission Key Laboratory for BiosafetyNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China

In October 2017,a small outbreak of echovirus 30(E30)associated with aseptic meningitis in nine cases occurred at a primary school in the Ningxia Hui Autonomous *** year,we observed a significant increase in E30 levels in an acute flaccid paralysis(AFP)case surveillance *** investigate their phylogenetic relationships,we determined the whole genomic sequences of 12 strains isolated from aseptic meningitis cases,AFP cases,and healthy *** found that the E30 strains circulating in Ningxia belong to two lineages(H and J).The strains isolated in 2010,2012,and 2016 belonged to the H *** 2017,a new lineage,J,emerged as the dominant *** trees were constructed based on the whole genome andP1,P2,andP3 regions;clustering with other types of enterovirus species B was found,suggesting that recombination events had *** recombination sites were mainly in regions2B,2C,*** study confirmed that the E30 strains in Ningxia in 2010,2012,and 2016 had different recombination patterns and were recombined with different *** 2017 epidemic E30 originated from another new lineage with a complex recombination pattern and formed an independent transmission chain in Ningxia.

关键词： Echovirus 30(E30) complete genome sequence Molecular epidemiology

Safety evaluation and complete genome analysis emphasis on extracellular polysaccharide of two strains of Limosilactobacillus fermentum MWLf-4 and Lactipiantibacillus plantarum MWLp-12 from human milk

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FOOD BIOSCIENCE 2023年第1期51卷 1190-1201页

作者： Wang, Yajuan Yang, Haoyu Mu, Guangqing Wu, Xiaomeng Dalian Polytech Univ Sch Food Sci & Technol Dalian 116000 Liaoning Peoples R China

In order to reduce the use of thickening agent in yogurt and increase the viscosity of fermented milk, we screened two probiotics from breast milk as co-cultured with commercial fermenting bacteria in the previous study, and found that the two strains (i.e. Limosilactobacillus fermentum MWLf-4 and Lactipiantibacillus plantarum MWLp-12) had a great ability to increase the viscosity of fermented milk. After that, in this paper we observed the extra-cellular polysaccharides of single strain fermented milk using inverted fluorescence microscope. Furthermore, the complete gene sequences and safety evaluation including antibiotic sensitivity test, hemolysis test and determination of amine in vitro of Limosilactobacillus fermentum MWLf-4 and Lactipiantibacillus plantarum MWLp-12 were carried out. As a conclusion, the two strains possess a better ability to produce extracellular poly-saccharide, and they are potentially safe strains. It is worth noting that the genes that produce exopoly-saccharides of tagE and glmU are found in Limosilactobacillus fermentum MWLf-4, and cps gene cluster and galE are found in Lactipiantibacillus plantarum MWLp-12. Therefore, this study provides a reliable theoretical basis for further elaborating the relationship between genes and functionality.

关键词： Human milk source probiotics complete genome sequence Safety evaluation Extracellular polysaccharide