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Gene characterization and phylogenetic analysis of four mitochondrial genomes in Caenogastropoda

Acta Oceanologica Sinica 2024年第2期43卷 137-150页

作者： Jiangyong Qu Wanqi Yang Xindong Teng Li Xu Dachuan Zhang Zhikai Xing Shuang Wang Xiumei Liu Lijun Wang Xumin Wang College of Life Science Yantai UniversityYantai 264005China Qingdao International Travel Healthcare Center Qingdao 266071China Qingdao Dagang Customs Qingdao 266071China

Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.

关键词： mitochondrial genome phylogenetic analysis Caenogastropoda

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phylogenetic analysis and arsenate reduction effect of the arsenic-reducing bacteria enriched from contaminated soils at an abandoned smelter site

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Journal of Environmental Sciences 2008年第12期20卷 1501-1507页

作者： ZHANG, Xuexia JIA, Yongfeng WANG, Xin XU, Liying Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110016 China Graduate University Chinese Academy of Sciences Beijing 100039 China

Microbial reduction of As(V)(i.e.,arsenate)plays an important role in arsenic(As)mobilization in aqueous environment.In this study,we investigated As(V)reduction characteristics of the bacteria enriched from the arsenic-contaminated soil at an abandoned smelter site.It was found that As(V)was completely reduced to As(III)(i.e.,arsenite)in 21 h.After 3-d incubation,a yellow solid was precipitated and the concentration of As(III)decreased sharply.After 150 h incubation,ca.65%of soluble arsenic was removed fro...

关键词： microbial reduction arsenic phylogenetic analysis

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phylogenetic and Comparative Genomic analysis of Lactobacillus fermentum Strains and the Key Genes Related to their Intestinal Anti-Inflammatory Effects

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Engineering 2022年第10期17卷 170-182页

作者： Yan Zhao Chengcheng Zhang Leilei Yu Fengwei Tian Jianxin Zhao Hao Zhang Wei Chen Qixiao Zhai State Key Laboratory of Food Science and Technology Jiangnan UniversityWuxi 214122China School of Food Science and Technology Jiangnan UniversityWuxi 214122China National Engineering Research Centre for Functional Food Jiangnan UniversityWuxi 214122China International Joint Research Laboratory for Probiotics Jiangnan UniversityWuxi 214122China Beijing Innovation Centre of Food Nutrition and Human Health Beijing Technology and Business UniversityBeijing 100048China

Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced.Pan-genomic and phylogenetic characterizations of these strains and four model strains(L.fermentum 3872,CECT5716,IF03956,and VRI003)were performed.phylogenetic analysis ind icated that there was no significant adaptive evolution between the genomes of L.fermentum strains and the geographical location,sex,ethnicity,and age of the hosts.Three L.fermentum strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type L.fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further investigated.Both L.fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar protection.The anti-inflammato ry mechanisms of L.fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)production.Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L.fermentum strains.

关键词： Lactobacillus fermentum Ulcerative colitis Anti-inflammation phylogenetic analysis Comparative genomic analysis

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Isolation and phylogenetic analysis of feline calicivirus strains from various region of China

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Animal Diseases 2022年第3期2卷 165-174页

作者： Longlong Cao Qiuyan Li Kaituo Shi Liting Wei Hehao Ouyang Zijun Ye Wenguang Du Jiawen Ye Xiaochen Hui Jiakang Li Shengbo Cao Dengyuan Zhou State Key Laboratory of Agricultural Microbiology Huazhong Agricultural UniversityWuhanChina College of Veterinary Medicine Huazhong Agricultural UniversityWuhanChina Wuhan Keqian Biology Co. LtdWuhanChina

Feline calicivirus(FCV)is an important feline pathogen mainly causing upper respiratory tract disease,conjunctivitis,and stomatitis,and it is classifed into genotype I and genotype II.To investigate the prevalence and molecular characteristics of FCV,this study collected 337 cat swab samples from animal hospitals in diferent regions of China from 2019 to 2021.The positive detection rate of FCV was 29.9%(101/337)by RT-PCR.Statistical analysis showed that FCV prevalence was signifcantly associated with living environment(p=0.0004),age(p=0.031)and clinical symptoms(p=0.00),but not with sex(p=0.092)and breed(p=0.171).The 26 strains of FCV were isolated using F81 cells.phylogenetic analysis showed that 10 isolates belonged to genotype I,and 16 isolates belonged to genotype II.These 26 isolates were highly genetically diverse,of which HB7 isolate had three same virulence-related amino acid loci with VSD strains.Potential loci distinguishing diferent genotypes were identifed from 26 isolates,suggesting the genetic relationship between diferent genotypes.In addition,selection pressure analysis based on capsid protein of 26 isolates revealed that the protein is under diversifying selection.This study reveals the genetic diversity of FCV and provides a reference for the screening of vaccine candidate strains and the development of vaccines with better cross-protection efects.

关键词： Feline Calicivirus Genetic diversity phylogenetic analysis Selection pressure analysis ORF2 gene

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phylogenetic analysis of mtDNA from the Ancient Human of Yuan Dynasty in Inner Mongolia in China

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Chemical Research in Chinese Universities 2006年第2期22卷 177-180页

作者： FU Yu-qin XU Xue-lian ZHANG Xiao-lei ZHANG Quan-chao ZHOU Hui ZHU Hong Ancient DNA Laboratory Research Center for Chinese Frontier Archaeology Jilin UniversityChangchun 130012 P. R. China College of Life Science Jilin University 130021 P. R. China

A study of the genetic structure of an ancient human excavated from the Yikeshu site of Yuanshangdu ancient city in Inner Mongolia and the relationships between the ancient population and the extant populations was carried out. Sequences of the control region and coding region of mtDNA from the ancient human were analyzed by using direct sequencing and restriction-fragment length polymorphism （RFLP） methods, phylogenetic analysis and multidimensional scaling analysis were also performed on the mtDNA data of the ancient population and 12 extant populations. These results show that the ancient individuals of Yikeshu site can be assigned to D, G, B and Z haplogroups that are prevalent in Duars and Mongolians from Inner Mongolia. The ancient population is also closer to Duar and Mongolian populations in genetic distance than other compared populations. This study reveals that the ancient population from Yikeshu site in the Yuan Dynasty shares a common ancestor with Mongolic-speaking Daur and Mongolian tribes.

关键词： MtDNA Polymorphism phylogenetic analysis

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Viromes of Haemaphysalis longicornis reveal different viral abundance and diversity in free and engorged ticks

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Virologica Sinica 2024年第2期39卷 194-204页

作者： Jian Xiao Xuan Yao Xuhua Guan Jinfeng Xiong Yaohui Fang Jingyuan Zhang You Zhang Abulimiti Moming Zhengyuan Su Jiayin Jin Yingying Ge Jun Wang Zhaojun Fan Shuang Tang Shu Shen Fei Deng Key Laboratory of Virology and Biosafety and National Virus Resource Center Wuhan Institute of VirologyChinese Academy of SciencesWuhan430071China Hubei Provincial Center for Disease Control and Prevention Wuhan430070China University of Chinese Academy of Sciences Beijing101408China Hubei Jiangxia Laboratory Wuhan430200China Xinjiang Key Laboratory of Vector-borne Infectious Diseases Urumqi830002China Current address:Department of Medical Laboratory The Second Affiliated HospitalHainan Medical UniversityHaikou57000China

Haemaphysalis longicornis ticks,commonly found in East Asia,can transmit various pathogenic viruses,includingthe severe fever with thrombocytopenia syndrome virus(SFTSV)that has caused febrile diseases among humansin Hubei Province.However,understanding of the viromes of H.longicornis was limited,and the prevalence ofviruses among H.longicornis ticks in Hubei was not well clarified.This study investigates the viromes of bothengorged(fed)and free(unfed)H.longicornis ticks across three mountainous regions in Hubei Province from 2019to 2020.RNA-sequencing analysis identified viral sequences that were related to 39 reference viruses belonging tounclassified viruses and seven RNA viral families,namely Chuviridae,Nairoviridae,Orthomyxoviridae,Parvoviridae,Phenuiviridae,Rhabdoviridae,and Totiviridae.Viral abundance and diversity in these ticks were analysed,andphylogenetic characteristics of the Henan tick virus(HNTV),Dabieshan tick virus(DBSTV),Okutama tick virus(OKTV),and Jingmen tick virus(JMTV)were elucidated based on their full genomic sequences.Prevalenceanalysis demonstrated that DBSTV was the most common virus found in individual H.longicornis ticks(12.59%),followed by HNTV(0.35%),whereas JMTV and OKTV were not detected.These results improve our understanding of H.longicornis tick viromes in central China and highlight the role of tick feeding status and geographyin shaping the viral community.The findings of new viral strains and their potential impact on public health raisethe need to strengthen surveillance efforts for comprehensively assessing their spillover potentials.

关键词： Ticks Virome Haemaphysalis longicornis phylogenetic analysis Viral abundance and diversity

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phylogenetic analysis and Expression Patterns of the MAPK Gene Family in Wheat (Triticum aestivum L.)

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Journal of Integrative Agriculture 2012年第8期11卷 1227-1235页

作者： LIAN Wei-wei TANG Yi-miao GAO Shi-qing ZHANG Zhao ZHAO Xin ZHAO Chang-ping Beijing Engineering and Technique Research Center of Hybrid Wheat Beijing Academy of Agricultural and Forestry Sciences Beijing 100097 P.R.China College of Life Science Capital Normal University Beijing 100048 P.R. China

Mitogen activated protein kinases （MAPK） cascades based on protein phosphorylation play an important role in plant growth and development. In this study, we have identified 15 putative members of the wheat MAPK gene （TaMPK） family through an in silico search of wheat expressed sequence tags （EST） databases based on the presence of amino acid sequence of Arabidopsis and rice MAPKs. phylogenetic analyses of MAPKs from wheat, rice and Arabidopsis genomes have classified them into seven subgroups （A, B, C, D, E, F, and G）. Using the available EST information as a source of expression data, the MAPK family genes from Triticum aestivum were detected in diverse tissues. Further expression analysis of the MAPKs in NCBI EST database revealed that their transcripts were most abundant in callus （20%）, followed by leaf （12%） and inflorescence （12%）. Most MAPK family genes showed some tissue specificity.

关键词： wheat MAPK EST phylogenetic analysis profile

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Epidemiological Surveillance: Genetic Diversity of Rotavirus Group A in the Pearl River Delta, Guangdong, China in 2019

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Biomedical and Environmental Sciences 2024年第3期37卷 278-293页

作者： JIANG Jie Ying LIANG Dan WANG Li XIAO Yun LIANG Yu Feng KE Bi Xia SU Juan XIAO Hong WANG Tao ZOU Min LI Hong Jian KE Chang Wen School of Public Health Shantou UniversityShantou 515063GuangdongChina Guangdong Provincial Center for Disease Control and Prevention Guangdong Workstation for Emerging Infectious Disease Control and PreventionGuangzhou 511430GuangdongChina Guangdong Provincial Key Laboratory of Virology Institute of Medical MicrobiologyJinan UniversityGuangzhou 510632GuangdongChina School of Public Health Sun Yat-sen UniversityGuangzhou 510275GuangdongChina School of Public Health Southern Medical UniversityGuangzhou 510515GuangdongChina Shantou University Medical College Shantou 515041GuangdongChina

Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.

关键词： Infectious diarrheal disease Rotavirus phylogenetic analysis Gene rearrangement Codon usage bias Genetic diversity

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Complete Mitochondrial Genome analysis of Daphniopsis tibetana(Branchiopoda:Diplostraca):New Insights into the Taxonomy of the Genus and Its phylogenetic Implications for Branchiopoda

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Journal of Ocean University of China 2022年第6期21卷 1622-1632页

作者： LIU Bingjian PENG Ying LIU Yifan LI Jiasheng ZHANG Kun CHEN Jian GONG Li LIU Liqin LÜZhenming ZHANG Chi National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China Institute of Fisheries Science Tibet Academy of Agricultural and Animal Husbandry SciencesLhasa 850002China Key Laboratory of Tropical Marine Bio-Resources and Ecology Chinese Academy of SciencesGuangzhou 510301China

Daphniopsis tibetana is widely distributed in Xinjiang,Qinghai,Tibet of China,as well as in Russia and India,which is the dominant zooplankton in many high-altitude(4000 m)salt lakes.D.tibetana can adapt to saline waters,whereas the other species of the superorder Cladocera can only inhabit in freshwater.However,the phylogenetic status of D.tibetana in Branchiopoda remains unclear primarily because of limited mitogenome.In this study,complete mitochondrial genome sequences of D.tibetana were sequenced and annotated for the first time to obtain a comprehensive understanding of its phylogenetic status.The complete mitogenome of D.tibetana is 16196 bp in length.It contains 37 genes,including two ribosomal RNAs(12S and 16S rRNAs)genes,22 transfer RNA(tRNA)genes,13 protein-coding genes,and one non-coding region.The overall base composition is 29.6%A,33.2%T,19.0%G,and 18.2%C with a high AT bias(62.8%).Except for trnS1(GCT),most tRNAs have a typical cloverleaf secondary structure.phylogenetic analysis based on maximum likelihood and Bayesian inference generates identical phylogenetic topology and shows the phylogenetic status of D.tibetana,which reconfirm the distinction between the genera Daphniopsis and Daphnia.Meanwhile,the class Branchiopoda is clustered into three clades(Anostraca,Notostraca,and Diplostraca)with high support values.These results provide not only a comprehensive understanding of the characteristics of D.tibetana mitogenome and its phylogenetic position in Diplostraca,but also information for future research on the phylogeny of Branchiopoda.

关键词： Daphniopsis tibetana mitogenome phylogenetic analysis Branchiopoda Diplostraca

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Characterization and phylogenetic analysis of a phenanthrene-degrading strain isolated from oil-contaminated soil

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Journal of Environmental Sciences 2004年第4期16卷 589-593页

作者： XIAYing MINHang LUZhen-mei YEYang-fang CollegeofLifeScience ZhejiangUniversityHangzhou310029China

Bacterium strain EVA17 was isolated from an oil-contaminated soil, and identified as Sphingomonas sp. based on analysis of 16S rDNA sequence,cellular fatty acid composition and physiological-chemical tests. The salicylate hydroxylase and catechol 2,3-dioxygenase(C23O) were detected in cell-free lysates, suggesting a pathway for phenanthrene catabolism via salicylate and catechol. Alignment showed that both of the C23O and GST genes of the strain EVA17 had high similarity with homologues of strains from genus Sphingomonas. The phylogenetic analysis based on 16S rDNA and C23O gene sequence indicated that EVA17 should be classified into genus Sphingomonas, although the two phylogenetic trees were slightly different from each other. The results of co-amplification and sequence determination indicated that GST gene should be located upstream of the C23O gene.

关键词： phenanthrene 16S rDNA glutathione S-transferase catechol 2,3-dioxygenase phylogenetic analysis

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