Volume 19 Issue 5
Oct.  2023
Turn off MathJax
Article Contents
Abstract
References
Related Articles
LIU Min, LIU Chang, LIU Guangfeng, ZHU Peng, XIE Keming, JIANG Jingzhe. Identification and evolutionary analysis of genome of oyster-associated Microviridae[J]. South China Fisheries Science, 2023, 19(5): 134-142. DOI: 10.12131/20230038
Citation: LIU Min, LIU Chang, LIU Guangfeng, ZHU Peng, XIE Keming, JIANG Jingzhe. Identification and evolutionary analysis of genome of oyster-associated Microviridae[J]. South China Fisheries Science, 2023, 19(5): 134-142. DOI: 10.12131/20230038
shu

Identification and evolutionary analysis of genome of oyster-associated Microviridae

  • 1.

    College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China

  • 2.

    South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory of South China Sea Fishery, Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China

  • 3.

    College of Life Science and Biopharmacy, Guangdong Pharmaceutical University, Guangzhou 510005, China

More Information
  • Received Date: March 06, 2023
  • Revised Date: June 04, 2023
  • Accepted Date: June 25, 2023
  • Available Online: June 29, 2023
    Graphical Abstract
    • Abstract

  • Oysters with filter feeding habits enrich a large number of pathogens including viruses in water, like a very valuable virus bank. To conduct an in-depth research on oyster-related viruses, we sequeced the Hong Kong oyster (Crassostrea hongkongensis) collected along the South China coast. After the quality control, assembly and taxonomy annotation of the sequencing data, we selected five genomic sequences which were identified as Microviridae for multi-dimensional analyses, such as host prediction, open reading frame and gene function prediction, phylogeny and three-dimensional structure prediction of major capsid proteins, evolutionary association between major capsid proteins and external scaffold proteins, as well as virus abundance analysis. The results show that the hosts of the five viruses were all Escherichia; one of the virus genome sequences was clustered in Bullavirinae branch, which indicates that it is a member of the subfamily; the other four genome sequences were not clustered into any known subfamilies so they should belong to a single unclassified subfamily; the relationship between the evolutionary tree of the main capsid proteins and external scaffold proteins indicates that the evolution rules of the two proteins were different.

    • FullText(HTML)
    • References (40)
  • [1]
    李辉尚, 李坚明, 秦小明, 等. 中国牡蛎产业发展现状、问题与对策:基于鲁、闽、粤、桂四省区的实证分析[J]. 海洋科学, 2017, 41(11): 125-129.
    [2]
    李晨, 谢晓晨, 王博, 等. 牡蛎细菌病的研究进展[J]. 环境生态学, 2022, 4(4): 59-64.
    [3]
    CHANG R Y, WONG J, MATHAI A, et al. Production of highly stable spray dried phage formulations for treatment of Pseudomonas aeruginosa lung infection[J]. Eur J Pharm Biopharm, 2017, 12(1): 1-13.
    [4]
    赵虹泽. 噬菌体对鸡白痢治疗效果评价及其对盲肠菌群的影响[D]. 武汉: 华中农业大学, 2022: 1-10.
    [5]
    DOSS J, CULBERTSON K, HAHN D, et al. A review of phage therapy against bacterial pathogens of aquatic and terrestrial organisms[J]. Viruses, 2017, 9(3): 50-60. doi: 10.3390/v9030050
    [6]
    PEDULLA M L, FORD M E, HOUTZ J M, et al. Origins of highly mosaic mycobacteriophage genomes[J]. Cell, 2003, 113(2): 171-182. doi: 10.1016/S0092-8674(03)00233-2
    [7]
    SALMOND G P, FINERAN P C. A century of the phage: past, present and future[J]. Nat Rev Microbiol, 2015, 13(12): 777-786. doi: 10.1038/nrmicro3564
    [8]
    GILDEA L, AYARIGA J A, ROBERTSON B K. Bacteriophages as biocontrol agents in livestock food production[J]. Microorganisms, 2022, 10(11): 2126-2145. doi: 10.3390/microorganisms10112126
    [9]
    DESNUES C, RODRIGUEZ-BRITO B, RAYHAWK S, et al. Biodiversity and biogeography of phages in modern stromatolites and thrombolites[J]. Nature, 2008, 452(7185): 340-343. doi: 10.1038/nature06735
    [10]
    ROSARIO K, DAYARAM A, MARINOV M, et al. Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta)[J]. J Gen Virol, 2012, 93(Pt 12): 2668-2681.
    [11]
    JIANG J Z, FANG Y F, WEI H Y, et al. A remarkably diverse and well-organized virus community in a filter-feeding oyster[J]. Microbiome, 2023, 11(1): 2-16. doi: 10.1186/s40168-022-01431-8
    [12]
    BRENTLINGER K L, HAFENSTEIN S, NOVAK C R, et al. Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus[J]. J Bacteriol, 2002, 184(4): 1089-1094. doi: 10.1128/jb.184.4.1089-1094.2002
    [13]
    QUAISER A, DUFRESNE A, BALLAUD F, et al. Diversity and comparative genomics of Microviridae in Sphagnum-dominated peatlands[J]. Front Microbiol, 2015, 6: 375-385.
    [14]
    ZHANG T, BREITBART M, LEE W H, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses[J]. PLoS Biol, 2006, 4(1): 3-12.
    [15]
    BREITBART M, HAYNES M, KELLEY S, et al. Viral diversity and dynamics in an infant gut[J]. Res Microbiol, 2008, 159(5): 367-373. doi: 10.1016/j.resmic.2008.04.006
    [16]
    BENBOW R M, HUTCHISON C A, FABRICANT J D, et al. Genetic map of bacteriophage φX174[J]. J Virol, 1971, 7(5): 549-558. doi: 10.1128/jvi.7.5.549-558.1971
    [17]
    CHEN S, ZHOU Y, CHEN Y, et al. Fastp: an ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics, 2018, 34(17): i884-i890. doi: 10.1093/bioinformatics/bty560
    [18]
    LI D, LIU C M, LUO R, et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph[J]. Bioinformatics, 2015, 31(10): 1674-1676. doi: 10.1093/bioinformatics/btv033
    [19]
    BUCHFINK B, XIE C, HUSON D H. Fast and sensitive protein alignment using DIAMOND[J]. Nat Methods, 2015, 12(1): 59-60. doi: 10.1038/nmeth.3176
    [20]
    HUSON D H, BEIER S, FLADE I, et al. MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data[J]. PLoS Comput Biol, 2016, 12(6): e1004957. doi: 10.1371/journal.pcbi.1004957
    [21]
    HYATT D, CHEN G L, LOCASCIO P F, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification[J]. BMC Bioinform, 2010, 11(1): 119-130. doi: 10.1186/1471-2105-11-119
    [22]
    关迎晖, 向勇, 陈康. 基于Gephi的可视分析方法研究与应用[J]. 电信科学, 2013,2 9(S1): 112-119.
    [23]
    KATOH K, STANDLEY D M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Mol Biol Evol, 2013, 30(4): 772-780. doi: 10.1093/molbev/mst010
    [24]
    CAPELLA-GUTIÉRREZ S, SILLA-MARTíNEZ J M, GABALDÓN T. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses[J]. Bioinformatics, 2009, 25(15): 1972-1973. doi: 10.1093/bioinformatics/btp348
    [25]
    NGUYEN L T, SCHMIDT H A, von HAESELER A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[J]. Mol Biol Evol, 2014, 32(1): 268-274.
    [26]
    LEE I, OUK KIM Y, PARK S C, et al. OrthoANI: an improved algorithm and software for calculating average nucleotide identity[J]. Int J Syst Evol Microbiol, 2016, 66(2): 1100-1103. doi: 10.1099/ijsem.0.000760
    [27]
    TISZA M J, BELFORD A K, DOMÍNGUEZ-HUERTA G, et al. Cenote-Taker 2 democratizes virus discovery and sequence annotation[J]. Virus Evol, 2021, 7(1): veaa100. doi: 10.1093/ve/veaa100
    [28]
    SHANG J, SUN Y. CHERRY: a computational method for accurate prediction of virus-prokaryotic interactions using a graph encoder-decoder model[J]. Brief Bioinform, 2022, 23(5): 182-198. doi: 10.1093/bib/bbac182
    [29]
    PATRO R, DUGGAL G, LOVE M I, et al. Salmon provides fast and bias-aware quantification of transcript expression[J]. Nat Methods, 2017, 14(4): 417-419. doi: 10.1038/nmeth.4197
    [30]
    HOPKINS M, KAILASAN S, COHEN A, et al. Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein[J]. Isme J, 2014, 8(10): 2093-2103. doi: 10.1038/ismej.2014.43
    [31]
    李灏, 丁子元, 徐林通, 等. 论我国水产养殖病害控制技术现状与发展趋势[J]. 农业与技术, 2015, 35(24): 171.
    [32]
    陈愿. 噬菌体在水产养殖业中的研究进展[J]. 水产学报, 2021, 45(9): 1605-1615.
    [33]
    ROHWER F, THURBER R V. Viruses manipulate the marine environment[J]. Nature, 2009, 459(7244): 207-212. doi: 10.1038/nature08060
    [34]
    ROUX S, ENAULT F, ROBIN A, et al. Assessing the diversity and specificity of two freshwater viral communities through metagenomics[J]. PLoS One, 2012, 7(3): e33641. doi: 10.1371/journal.pone.0033641
    [35]
    KRUPOVIC M, FORTERRE P. Microviridae goes temperate: microvirus-related proviruses reside in the Genomes of Bacteroidetes[J]. PLoS One, 2011,6(5): e19893.
    [36]
    李振, 张建城, 曹振辉, 等. 噬菌体控制主要水产养殖类致病菌的研究进展[J]. 畜牧与兽医, 2015, 47(8): 138-143.
    [37]
    PENG Y, JIN Y, LIN H, et al. Application of the VPp1 bacteriophage combined with a coupled enzyme system in the rapid detection of Vibrio parahaemolyticus[J]. J Microbiol Methods, 2014, 98(3): 99-104.
    [38]
    GAUDU P, YAMAMOTO Y, JENSEN P R, et al. Genetics of Lactococci[J]. Microbiol Spectr, 2019, 7(4): 361-362.
    [39]
    洪宝华, 马荣荣, 袁娜. 养殖梭鱼格氏乳球菌的分离鉴定及致病性研究[J]. 农业生物技术学报, 2020, 28(8): 1458-1470.
    [40]
    ZHU P, LIU G F, LIU C, et al. Novel RNA viruses in oysters revealed by virome[J]. iMeta, 2022, 1(4): e65.
    • Related Articles

  • Related Articles

    [1]PEI Ruonan, ZHAI Honglei, QI Bo, YANG Xianqing. Optimization of multi-enzymatic extraction of polysaccharide from Gelidium amansii by response surface methodology[J]. South China Fisheries Science, 2019, 15(6): 88-95. DOI: 10.12131/20190081
    [2]WANG Xiaohui, QI Bo, YANG Xianqing, YANG Shaoling, MA Haixia, DENG Jianchao. Optimization of enzymatic hydrolysis of protein in abandoned Porphyra haitanensis by response surface methodology and study on antioxidant activity of its hydrolysate[J]. South China Fisheries Science, 2019, 15(2): 93-101. DOI: 10.12131/20180099
    [3]YU Futian, CEN Jianwei, LI Laihao, YANG Xianqing, HANG Hui, HAO Shuxian, WEI Ya, ZHAO Yongqiang, LIN Zhi. Response surface methodology for optimization of sterilization effect on tilapia fillet with slightly acidic electrolyzed water[J]. South China Fisheries Science, 2019, 15(1): 77-84. DOI: 10.12131/20180164
    [4]ZHONG Zhihong, WANG Fei, CHEN Yonggui, DENG Hengwei, WANG Shifeng, SUN Yun, CHEN Xuefen, GUO Weiliang, ZHOU Yongcan. Synergism between Fructus mume and antibiotics against Vibrio harveyi based on response surface methodology[J]. South China Fisheries Science, 2018, 14(6): 81-88. DOI: 10.12131/20180056
    [5]LI Shasha, CAO Yucheng, HU Xiaojuan, LI Zhuojia, XU Yu, YANG Keng, XU Chuangwen, WEN Guoliang. Optimization for cultivation parameters of Bacillus sp. A4 using response surface methodology[J]. South China Fisheries Science, 2017, 13(5): 85-93. DOI: 10.3969/j.issn.2095-0780.2017.05.012
    [6]CHEN Kang, DAI Zhiyuan, SHEN Qing, HUANG Yaowen. Extraction of phospholipid from Euphausia superba by response surface method and determination of phospholipid molecular species[J]. South China Fisheries Science, 2017, 13(3): 104-112. DOI: 10.3969/j.issn.2095-0780.2017.03.014
    [7]ZHAO Donghao, WANG Xufeng, WANG Qiang, LI Zhiguang, HUANG Ke, LI Liudong. Influence of solvent on nitrofuran metabolites response by liquid chromatography-tandem mass spectrometry[J]. South China Fisheries Science, 2016, 12(6): 108-114. DOI: 10.3969/j.issn.2095-0780.2016.06.014
    [8]ZHAO Donghao, LI Zhiguang, WANG Xufeng, WANG Qiang, LI Yongxian, HUANG Ke, LI Liudong. Optimization of determination of nitrofuran metabolites in aquatic products by liquid chromatography tandem mass spectrometry[J]. South China Fisheries Science, 2015, 11(6): 58-64. DOI: 10.3969/j.issn.2095-0780.2015.06.008
    [9]WANG Zhongliang, HUANG Jiansheng, ZHANG Jiandong, CHEN Gang. Combined effect of light intensity and salinity on hatchability of Artemia cysts based on response surface methodology[J]. South China Fisheries Science, 2014, 10(3): 80-85. DOI: 10.3969/j.issn.2095-0780.2014.03.012
    [10]QI Bo, LI Laihao, YANG Xianqing, CHENG Shengjun, LIU Gang, LI Zhandong. Optimization technology of alkali processing of Eucheuma carrageenan by response surface methodology[J]. South China Fisheries Science, 2011, 7(6): 26-34. DOI: 10.3969/j.issn.2095-0780.2011.06.005

  • Cited by

    Periodical cited type(2)

    1. 吴燕燕，王悦齐，张涛，王迪，郑镇雄. 不同致死条件对冷鲜石斑鱼肉品质的影响. 上海海洋大学学报. 2023(02): 377-386 .
    2. 王雪松，谢晶. 竹荚鱼浸渍冻结液配方的优化与应用效果. 食品与发酵工业. 2021(19): 195-200 .

    Other cited types(3)

Catalog

    Get Citation
    PDF
    XML
    Article views PDF downloads Cited by(5)
    Related

    Supported by: Beijing Renhe Information Technology Co., Ltd.  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return