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evolutionary analysis of Omicron variant BF.7 and BA.5.2 pandemic in China

Journal of Biosafety and Biosecurity 2023年第1期5卷 14-20页

作者： Yamin Sun Min Wang Wenchao Lin Wei Dong Jianguo Xu Research Institute of Public Health Nankai UniversityTianjinPR China Research Center for Functional Genomics and Biochip TianjinPR China c State Key Laboratory for Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 202206PR China TEDA Institute of Biological Sciences and Biotechnology Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationNankai UniversityTianjinPR China Research Units of Discovery of Unknown Bacteria and Function Chinese Academy of Medical SciencesBeijing 100730PR China

On December 7,2022,China adjusted public health control measures,there have been widespread of SARS-CoV-2 infections in Chinese *** the number of infected people increased,the mutation probability of SARS-CoV-2 is also ***,it is of great importance to monitor SARS-CoV-2 variants and its mutations in *** this current study,665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants;to determine the composition of variants in China across different provinces;and analyze specific mutation frequency,focusing on 12 immune escape *** results showed that no new mutations were generated on the 12 immune escape *** evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites,officially named BF.7.14 by *** variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in *** evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants,named BA.5.2.48 and BA.5.2.49 by PANGO,*** variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic ***,this study showed that current epidemic variants in China were already circulating in other countries,and there were no additional mutations on immune escape residues that could pose a threat to other countries.

关键词： SARS-CoV-2 Immune escape evolutionary analysis

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evolutionary analysis and lineage designation of SARS-CoV-2 genomes

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Science Bulletin 2021年第22期66卷 2297-2311,M0004页

作者： Xiaolu Tang Ruochen Ying Xinmin Yao Guanghao Li Changcheng Wu Yiyuli Tang Zhida Li Bishan Kuang Feng Wu Changsheng Chi Xiaoman Du Yi Qin Shenghan Gao Songnian Hu Juncai Ma Tiangang Liu Xinghuo Pang Jianwei Wang Guoping Zhao Wenjie Tan Yaping Zhang Xuemei Lu Jian Lu State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyCenter for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming 650223China Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100101China Yuxi Rongjian Information Technology Co. Ltd.Yuxi 653100China State Key Laboratory of Microbial Resources(SKLMR) The Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China The Microresource and Big Data Center The Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical SciencesWuhan 430071China Beijing Center for Disease Prevention and Control(CDC)&Research Center for Preventive Medicine of Beijing Beijing 100013China NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China

The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global *** the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly *** improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 *** divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and ***,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic *** lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major *** also provide a companion website(***)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage ***,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s *** efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.

关键词： COVID-19 evolutionary analysis Compensatory advantageous mutation Adaptive evolution Lineage designation

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Chromosome reassignment and evolutionary analysis of the Wcs19and Wcor15genes in wheat

Chromosome reassignment and evolutionary analysis of the Wcs...

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第六届全国小麦基因组学及分子育种大会

作者： Fangfang Liu Hongqi Si Cheng Chang Haiping Zhang Chuanxi Ma School of Agronomy Anhui Agricultural University Key Laboratory of wheat Biology and Genetic Improvement on South Yellow & Huai River valley Ministry of Agriculture

Wcor15 and Wcs19 are the member of the cold-responsive(Cor) gene family,which could encode the chloroplast-targeted protein when expose to low temperature,play an important roles in the cold hardiness of *** results have shown that both of the Wcor15 and Wcs19 were located on the group 2 *** the same time,the WCOR15 and WCS19 belong to the late embryogenesis abundant(LEA) 3-Like 2 *** research the assignment of Wcs19 and Wcs15 genes in the group 2 chromosomes and evolutionary relationship during wheat allopolyploidization,the two genes were amplified and directly sequenced from the hexaploid(common) wheat,tetraploid species and diploid *** results of genes sequences analysis showed that Wcs15 and Wcs19 were very conservative among hexaploid wheat varieties with different geographical areas,tetraploid species and diploid *** analyzing the nulli-tetrasomic lines of *** Spring,we highlighted that Wcs15,Wcs19 a and Wcs19 bwere found in the line with the exception of nullisomic2A-tetrasomic 2B(N2A-T2B),N2B-T2 A and N2D-T2 B *** further evolutionary analysis demonstrated that Wcs15 was assigned to chromosome 2AL,Wcs19 a was predominated in chromosome 2BL and Wcs19 b was located on chromosome 2DL which was confirmed by ENA sequence *** the same time,they harbored highly similar the N-Terminal ***15,Wcs19 a and Wcs19 b might be three homologous genes located on the same positions of the wheat genome 2 A,2B and 2D *** study provides a basis for more detailed structural analysis of chloroplast-targeted protein in wheat.

关键词： wheat Wcs19 Wcor15 chromosome assignment evolutionary analysis

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evolutionary and Functional analysis of the Key Pluripotency Factor Oct4 and Its Family Proteins

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Journal of Genetics and Genomics 2013年第8期40卷 399-412页

作者： Xinmin Zhang Yuzhen Ma Xiuying Liu Qi Zhou Xiu-Jie Wang Computer & Information Engineering College Inner Mongolia Normal University Centre of Reproductive Medicine Inner Mongolia Hospital State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences University of Chinese Academy of Sciences State Key Laboratory of Reproductive Biology Institute of ZoologyChinese Academy of Sciences

Oct4 is one of the key pluripotent factors essential for embryonic stem cells and induced pluripotent stem （iPS） cells. Oct4 belongs to the POU domain family, which contains multiples genes with various important functions. Although the function of Oct4 has been extensively studied, detailed comparison of Oct4 with other POU family genes and their evolutionary analysis are still lacking. Here, we systematically identified POU family genes from lower to higher animal species. We observed an expansion of POU family genes in vertebrates, with an additional increment in mammalian genomes. We analyzed the phylogenetic relationship, tissue specific expression profiles and regulatory networks of POU family genes of the human genome, and predicted the putative binding microRNAs of human POU family genes. These results provide the first comprehensive evolutionary and comparative analysis of POU family genes, which will help to better understand the relationships among POU family genes and shed light on their future functional studies.

关键词： Oct4 Induced pluripotent stem cell POU family MicroRNA evolutionary analysis

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Mayaro virus infection, the next epidemic wave after Zika?evolutionary and structural analysis

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Asian Pacific Journal of Tropical Medicine 2018年第3期11卷 194-201页

作者： Eleonora Cella Marta Giovanetti Teresa Milano Marta Fogolari Francesco Garilli Ivailo Alexiev Riccardo Bazzardi Marco Salemi Luiz Carlos Junior Alcantara Silvia Angeletti Stefano Pascarella Massimo Ciccozzi Public Health and Infectious Diseases Sapienza University Unit of Clinical Laboratory Science University Campus Bio-Medico of Rome Fundao Oswaldo Cruz University of Rome"Tor Vergata" Dipartimento di Scienze Biochimiche"A.Rossi Fanelli" Universita La Sapienza Department of Medicine University Campus Bio-Medico of Rome National Reference Laboratory of HIV National Center of Infectious and Parasitic Diseases Department of Food Hygiene Experimental Zooprophylactic Institute of Sardinia Emerging Pathogens Institute Unirersity of Florida

Objective: To evaluate the evolution of the pathogen Mayaro virus, causing Mayaro fever(a mosquito-borne disease) and to perform selective pressure analysis and homology ***: Nine different datasets were built, one for each protein(from protein C to non-structural protein 4) and the last one for the complete genome. Selective pressure and homology modelling analyses were applied. Results: Two main clades(A and B) were pointed in the maximum likelihood tree. The clade A included five Brazilian sequences sampled from 1955 to 2015. The Brazilian sequence sampled in 2014 significantly clustered with the Haitian sequence sampled in 2015. The clade B included the remaining 27 sequences sampled in the Central and Southern America from 1957 to 2013. Selective pressure analysis revealed several sites under episodic diversifying selection in envelope surface glycoprotein El, non-structural protein 1 and nonstructural protein 3 with a posterior probability P≤0.01. Homology modelling showed different sites modified by selective pressure and some protein-protein interaction sites at high interaction propensity. Conclusion: Maximum likelihood analysis confirmed the Mayaro virus previous circulation in Haiti and the successful spread to the Caribbean and USA. Selective pressure analysis revealed a strong presence of negatively selected sites, suggesting a probable purging of deleterious polymorphisms in functional genes. Homology model showed the position 31, under selective pressure, located in the edge of the ADP-ribose binding site predicting to possess a high potential of protein-protein interaction and suggesting the possible chance for a protective vaccine,thus preventing Mayaro virus urbanization as with Chikungunya virus.

关键词： Mayaro virus Proteins evolutionary analysis

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Genome wide investigation of Hsf gene family in Phoebe bournei:identification,evolution,and expression after abiotic stresses

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Journal of Forestry Research 2024年第5期35卷 201-215页

作者： Wenhai Liao Xinghao Tang Jingshu Li Qiumian Zheng Ting Wang Shengze Cheng Shiping Chen Shijiang Cao Guangqiu Cao College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002People’s Republic of China University Key Laboratory of Forest Stress Physiology Ecology and Molecular Biology of Fujian ProvinceFuzhou 350002People’s Republic of China Fujian Academy of Forestry Sciences Fuzhou 350002People’s Republic of China College of Plant Protection Fujian Agriculture and Forestry UniversityFuzhou 350002People’s Republic of China

Heat shock transcription factors(Hsfs)have important roles during plant growth and development and responses to abiotic *** identification and func-tion of Hsf genes have been thoroughly studied in various herbaceous plant species,but not woody species,especially Phoebe bournei,an endangered,unique species in *** this study,17 members of the Hsf gene family were identi-fied from *** using bioinformatic ***-netic analysis indicated that PbHsf genes were grouped into three subfamilies:A,B,and *** motifs,three-dimensional structure,and physicochemical properties of the PbHsf proteins were also *** structure of the PbHsf genes varied in the number of exons and ***-diction of cis-acting elements in the promoter region indi-cated that PbHsf genes are likely involved in responses to plant hormones and stresses.A collinearity analysis dem-onstrated that expansions of the PbHsf gene family mainly take place via segmental *** expression levels of PbHsf genes varied across different plant *** the basis of the expression profiles of five representative PbHsf genes during heat,cold,salt,and drought stress,PbHsf pro-teins seem to have multiple functions depending on the type of abiotic *** systematic,genome-wide investigation of PbHsf genes in *** and their expression patterns provides valuable insights and information for further func-tional dissection of Hsf proteins in this endangered,unique species.

关键词： Phoebe bournei Hsf gene family evolutionary analysis Expression mechanism Abiotic stresses

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水稻黑条矮缩病毒S6片段的序列多样性与进化分析

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植物病理学报 2023年第1期53卷 146-150页

作者：王馨玉许振南周羽翁建峰郭长虹李新海哈尔滨师范大学生命科学与技术学院哈尔滨150025 中国农业科学院作物科学研究所北京100081 东北农业大学农学院哈尔滨150030

0 引言植物RNA病毒在进化中具有快速变异的能力,有利于病毒扩大寄主范围甚至进化为新病毒[1]。突变和重组是植物RNA病毒变异和遗传多样性的共同进化因素,是群体基因变异的最初来源[2]。由灰飞虱传播的水稻黑条矮缩病毒(Rice black strea... 详细信息

0 引言植物RNA病毒在进化中具有快速变异的能力,有利于病毒扩大寄主范围甚至进化为新病毒[1]。突变和重组是植物RNA病毒变异和遗传多样性的共同进化因素,是群体基因变异的最初来源[2]。由灰飞虱传播的水稻黑条矮缩病毒(Rice black streaked dwarf virus, RBSDV) 属于呼肠孤病毒科(Reoviridae)斐济病毒属(Fijivirus),能引发玉米粗缩病和水稻黑条矮缩病。

关键词： rice black-streaked dwarf virus silencing inhibitor P6 genetic variation evolutionary analysis

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OsNPF3.1,a member of the NRT1/PTR family,increases nitrogen use efficiency and biomass production in rice

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The Crop Journal 2023年第1期11卷 108-118页

作者： Xinghai Yang Baoxuan Nong Can Chen Junrui Wang Xiuzhong Xia Zongqiong Zhang Yu Wei Yu Zeng Rui Feng Yanyan Wu Hui Guo Haifeng Yan Yuntao Liang Shuhui Liang Yong Yan Danting Li Guofu Deng Guangxi Key Laboratory of Rice Genetics and Breeding Rice Research InstituteGuangxi Academy of Agricultural SciencesNanning 530007GuangxiChina Guangxi Key Laboratory for Polysaccharide Materials and Modifications School of Marine Sciences and BiotechnologyGuangxi University for NationalitiesNanning 530006GuangxiChina Biotechnology Research Institute Guangxi Academy of Agricultural SciencesNanning 530007GuangxiChina Sugarcane Research Institute Guangxi Academy of Agricultural SciencesNanning 530007GuangxiChina Microbiology Research Institute Guangxi Academy of Agricultural SciencesNanning 530007GuangxiChina

The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental *** the N use efficiency(NUE)of rice varieties is crucial for sustainable *** we report the cloning and characterization of OsNPF3.1,a gene that controls rice *** amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated ***3.1,which is expressed mainly in the aerial parts of rice,also affects rice plant height,heading date,and thousand-grain *** OsNPF3.1 protein is located in the plasma *** OsNPF3.1 was subjected to artificial selection,two naturally varying loci were associated with NUE,of which OsNPF3.1Chr6_8741040differed between indica and japonica ***3.1 can be used as a new target gene for breeding rice varieties with high NUE.

关键词： Rice OsNPF3.1 Functional analysis evolutionary analysis Natural variation

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Systematic Identification of Rice ABC1 Gene Family and Its Response to Abiotic Stress

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Rice science 2011年第3期18卷 167-177页

作者： Qing-song GAO Dan ZHANG Liang XU Chen-wu XU Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of Ministry of Education Yangzhou University Yangzhou 225009 China

Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress response. Here, we present the systematic identification of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes. A total of 15 and 17 ABC1 genes from the rice and Arabidopsis genomes, respectively, were identified using a bioinformatics approach. Phylogenetic analyses of these proteins suggested that the divergence of this family had occurred and their main characteristics were established before the monocot-dicot split. Indeed, species-specific expansion contributed to the evolution of this family in rice and Arabidopsis after the monocot-dicot split. Intron/exon structure analysis indicated that most of the orthologous genes had similar exon sizes, but diverse intron sizes, and the rice genes contained larger introns, moreover, intron gain was an important event accompanying the recent evolution of the rice ABC1 family. Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids in the ABC1 domain. Online subcellular localization predicted that nine rice ABC1 proteins were localized in chloroplasts. Real-time RT-PCR established that the rice ABC1 genes were primarily expressed in leaves and the expression could be modulated by a broad range of abiotic factors such as H2O2, abscisic acid, low temperature, drought, darkness and high salinity. These results reveal that the rice ABC1 gene family plays roles in the environmental stress response and specific biological processes of rice.

关键词： rice activity of bc1 complex gene evolutionary analysis abiotic stress expression analysis gene function

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Molecular epidemiology of Bombyx mori nucleopolyhedrovirus in Yunnan sericulture region, China

Molecular epidemiology of Bombyx mori nucleopolyhedrovirus i...

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2019年全国蚕病理学与病虫害防控学术研讨会

作者：张永红 Fenfen Tang Yulan Shao Feng Zhu 白兴荣 Institute of Sericulture and Apiculture Yunnan Academy of Agricultural Science

Sericultural production is seriously influenced by the blood pathogens of grasserie, Bombyx mori nucleopolyhedrovirus（BmNPV）. In order to investigate the infectious condition and define an effective control method for BmNPV. 233 from 240 suspected samples infected with BmNPV were detected using PCR identification. One sample was selected from each county in the positive sample collection area, 56 isolates of which were used as experimental objects. The homology of the bro-d nucleotide sequence was at least 91% among the 56 BmNPV isolates. However, the conserved 7 amino acids（percentage of amino acid constant sites, PAACS） at the position 217 to 224 were absent for YNQJLL001 and YNZTQJ074 pandemic isolates. Phylogenetic tree analysis of bro-d gene separated the BmNPV isolates from Yunnan into 4 main clades: I, II, III, and IV. Clade I was the dominant clade containing 32 local epidemic isolates. Clades II, III, and IV contained 5, 16 and 3 pandemic isolates,respectively. Geographical distribution of clade I in Yunnan showed a concentrated pattern, while the remaining members of the other three clades depicted no direct contact in relation to their geographical positions. This study may provide valuable molecular types on BmNPV isolate distribution in the silkworm-raising regions, also be helpful for evaluating BmNPV pathogenesis and epidemic situations in the Yunnan sericulture region.

关键词： Bombyx mori nucleopolyhedrovirus bro-d evolutionary analysis BmNPV

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