留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

新型牡蛎相关圆环病毒基因组的鉴定

杨李玲 郭迎香 位红颖 王萌 方艺菲 朱鹏 姜敬哲

杨李玲, 郭迎香, 位红颖, 王萌, 方艺菲, 朱鹏, 姜敬哲. 新型牡蛎相关圆环病毒基因组的鉴定[J]. 南方水产科学. doi: 10.12131/20210260
引用本文: 杨李玲, 郭迎香, 位红颖, 王萌, 方艺菲, 朱鹏, 姜敬哲. 新型牡蛎相关圆环病毒基因组的鉴定[J]. 南方水产科学. doi: 10.12131/20210260
YANG Liling, GUO Yingxiang, WEI Hongying, WANG Meng, FANG Yifei, ZHU Peng, JIANG Jingzhe. Identification of a novel oyster-related circovirus genome compa-rative genome analysis of oyster-related circoviruses[J]. South China Fisheries Science. doi: 10.12131/20210260
Citation: YANG Liling, GUO Yingxiang, WEI Hongying, WANG Meng, FANG Yifei, ZHU Peng, JIANG Jingzhe. Identification of a novel oyster-related circovirus genome compa-rative genome analysis of oyster-related circoviruses[J]. South China Fisheries Science. doi: 10.12131/20210260

新型牡蛎相关圆环病毒基因组的鉴定

doi: 10.12131/20210260
基金项目: 国家自然科学基金面上项目“南海代表性贝类生物的病毒群体结构、功能及其驱动因素研究”(31972847);广东省省级现代农业产业技术体系“水产疫病监测与综合防控共性关键技术研发创新团队”(2019KJ141);中国水产科学研究院科技创新团队项目——贝类病害与生态防控创新团队 (2020TD42, 2021SD05)
详细信息
    作者简介:

    杨李玲 (1997—),女,硕士研究生,研究方向为渔业生物病害防治。E-mail: 2534118522@qq.com

    通讯作者:

    姜敬哲 (1980—),男,研究员,博士,从事渔业生物病害防治研究。Email: jingzhejiang@hotmail.com

  • 中图分类号: S 917.4

Identification of a novel oyster-related circovirus genome compa-rative genome analysis of oyster-related circoviruses

  • 摘要: 病原基因组信息的匮乏是牡蛎病害研究进展缓慢的主要原因之一。为鉴定更多牡蛎相关病毒,基于前期研究获得的华南沿海多地养殖的香港牡蛎 (Crassostrea hongkongensis) 病毒组测序数据进行质控、组装、物种注释后,挑选出其中疑似圆环病毒基因组序列进行进化树构建、基因组比较、蛋白结构域分析、三维结构预测和病毒丰度分析,在养殖牡蛎体内鉴定到了5个序列完整的新型牡蛎相关圆环病毒基因组,且5个病毒基因组在多个样品中存在。结果显示,5条病毒序列与已知的圆环病毒聚类在一个大的分支,说明其为圆环病毒科成员;5条病毒基因组序列均含有一个复制酶蛋白基因,且均与节肢动物圆环病毒复制酶蛋白序列最为相似;5条序列与另外7条公共数据库检索到的序列形成了一个独立的子分支,且该分支的序列来源多为动物相关样品。基于结构域分析软件 (SMART) 鉴定到多数序列中存在复制酶的保守结构域。
  • 图  1  单链DNA病毒基因组进化树 (VIPtree)

    Figure  1.  Phylogenetic tree of single-stranded DNA virus genome (VIPtree)

    图  2  牡蛎相关圆环病毒基因组与近源基因组序列构建的系统发育树

    Figure  2.  Phylogenetic tree of five oyster-related circoviruses and relative viral genome sequences

    图  3  圆环病毒基因组序列间的ANI (a) 和复制酶蛋白序列间的AAI (b)

    Figure  3.  ANI value among genomic sequences (a) and AAI value among replication proteins of circoviruses (b)

    图  4  牡蛎相关圆环病毒比较基因组分析图

    Figure  4.  Comparative genome analysis of oyster-related circoviruses

    图  5  牡蛎相关圆环病毒复制酶蛋白进化树

    Figure  5.  Phylogenetic tree of replication proteins of oyster-related circoviruses

    图  6  牡蛎相关圆环病毒复制酶蛋白序列比对

    Figure  6.  Sequence alignment of oyster-related circoviruses

    图  7  牡蛎相关圆环病毒复制酶蛋白三维结构预测图

    Figure  7.  Three-dimensional structure prediction of replication protein of oyster-related circoviruses

    表  1  牡蛎相关圆环病毒基因组信息

    Table  1.   Genome information of oyster-related circoviruses

    重叠群ID
    Contig ID

    Family
    基因组长度
    Genome length/kb
    复制酶蛋白开放阅读框位置
    Location of replication protein ORF
    衣壳蛋白开放阅读框位置
    Location of capsid protein ORF
    ML2-k141_11943 圆环病毒科 2 281 1~744 1 015~1 968
    ML2-k141_27933 圆环病毒科 2 170 335~1 102 1 338~1 946
    QZd1-k141_2132 圆环病毒科 1 942 179~976 1 303~1 941
    T5S3-k141_267932 圆环病毒科 2 137 1~816 951~1 841
    ZHd1-k141_220676 圆环病毒科 1 938 659~1 567 3~503
    下载: 导出CSV

    表  2  牡蛎相关圆环病毒丰度分析

    Table  2.   Analysis of abundance of oyster-related circovirus virus

    样本ID
    Sample ID
    病毒基因组ID Genome of virus ID
    ML2-k141_27933ZHd1-k141_220676ML2-k141_11943T5S3-k141_267932QZd1-k141_2132
    ChTW1511Rc 0 0 0 0 0
    ChYJ1509Da 0 0 0 76.93 542.87
    ChYJ1509Ra 0 0 0 0 0
    ChYJ1509Rb 0 0 0 0 0
    ChYJ1509Rc 0 1.36 0 0 0
    ChZH1511Da 0 55.17 0 0.69 1.51
    GX170519 0 0.22 0 0 0
    K1ZY170525 0 0 0.05 0.24 0
    ML1 148.67 0 2080.33 0 0
    ML2 12.46 0 193.02 0 0
    ML3 134.13 0.23 1505.51 0 0
    S5-D-2 0 0 0 0 0
    T2S170523 0 0 0 0.01 0.49
    T4S170523 0 0.01 0 0.29 0.21
    T5S170523 0 0.02 0 6.22 0.79
    T6S170523 0.36 0 0 0 0
    T8S170523 0 0 0 0.24 0.04
    下载: 导出CSV
  • [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] FARLEY C A, BANFIELD W G, KASNIC G J R, FOSTER W S. Oyster herpes-type virus[J]. Science, 1972, 178(4062): 759-760. doi: 10.1126/science.178.4062.759
    [3] MARTENOT C, TRAVAILLÉ E, LETHUILLIER O, et al. Genome exploration of six variants of the otreid hrpesvirus 1 and characterization of large deletion in OsHV-1μvar specimens[J]. Virus Res, 2013, 178(2): 462-470. doi: 10.1016/j.virusres.2013.08.006
    [4] MARTENOT C, LETHUILLIER O, FOUROUR S, et al. Detection of undescribed ostreid herpesvirus 1 (OsHV-1) specimens from Pacific oyster, Crassostrea gigas[J]. J Invertebr Pathol, 2015, 132: 182-189. doi: 10.1016/j.jip.2015.10.005
    [5] RENAULT T, NOVOA B. Viruses infecting bivalve molluscs[J]. Aquat Living Resour, 2004, 17(4): 397-409. doi: 10.1051/alr:2004049
    [6] DELMOTTE J, CHAPARRO C, GALINIER R, et al. Contribution of viral genomic diversity to oyster susceptibility in the Pacific oyster mortality syndrome[J]. Front Microbiol, 2020, 11: 1579. doi: 10.3389/fmicb.2020.01579
    [7] GUO X, FORD S E. Infectious diseases of marine molluscs and host responses as revealed by genomic tools[J]. Phil Trans Royal Soc Lond, 2016, 371(1689): 20150206. doi: 10.1098/rstb.2015.0206
    [8] BRUM J R, IGNACIO-ESPINOZA J C, ROUX S, et al. Patterns and ecological drivers of ocean viral communities[J]. Science, 2015, 348(6237): 1261498-1261498. doi: 10.1126/science.1261498
    [9] ZHANG X M, HUANG S B, JIN T, et al. Discovery and high prevalence of phasi charoen-like virus in field-captured Aedes Aegypti in South China[J]. Virology, 2018, 523: 35-40. doi: 10.1016/j.virol.2018.07.021
    [10] FILIPASILVA A, PARREIRA R, MARTÍNEZPUCHOL S, et al. The unexplored virome of two atlantic coast fish: contribution of next-generation sequencing to fish virology[J]. Foods (Basel, Switzerland), 2020, 9(11): 1634.
    [11] CALLANAN J, STOCKDALE S R, SHKOPOROV A, et al. Biases in viral metagenomics-based detection, cataloguing and quantification of bacteriophage genomes in human faeces, a review[J]. Microorganisms, 2021, 9(3): 524. doi: 10.3390/microorganisms9030524
    [12] 方艺菲. 华南沿海牡蛎体内病毒多样性及群落结构研究[D]. 上海: 上海海洋大学, 2021: 1-62.
    [13] 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
    [14] 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.
    [15] TING H F, SADAKANE K, LUO R B, et al. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices[J]. Methods: Companion Methods Enzymol, 2016, 102: 3-11. doi: 10.1016/j.ymeth.2016.02.020
    [16] BUCHFINK B, XIE C, HUSON D H. Fast and sensitive protein alignment using diamond[J]. Nat Methods, 2015, 12: 59-60. doi: 10.1038/nmeth.3176
    [17] DANIEL H H, SINA B, ISABELL F, et al. MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data[J]. PLoS, 2016, 12(6): e1004957.
    [18] NISHIMURA Y, YOSHIDA T, KURONISHI M, et al. ViPTree: the viral proteomic tree server[J]. Bioinformatics, 2017, 33(15): 2379-2380. doi: 10.1093/bioinformatics/btx157
    [19] KATOH K, STANDLEY D M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Mol Bilol Evol, 2013, 30(4): 772-780. doi: 10.1093/molbev/mst010
    [20] SALVADOR C R, JOSÉ M S N, TONI G N. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses[J]. Bioinformatics, 2009, 25(15): 1972-1973. doi: 10.1093/bioinformatics/btp348
    [21] TAMURA K, STECHER G, KUMAR S. MEGA11: molecular evolutionary genetics analysis version 11[J]. Mol Biol Evol, 2021, 38(7): 3022-3027. doi: 10.1093/molbev/msab120
    [22] 米晓云, 吴建勇, 马文戈, 等. 鸽圆环病毒新疆株全基因组克隆与序列分析[J]. 塔里木大学学报, 2021, 33(1): 1-8. doi: 10.3969/j.issn.1009-0568.2021.01.001
    [23] ROB P, GEET D, MICHAEL I L, et al. Salmon provides fast and bias-aware quantification of transcript expression[J]. Nature Methods, 2017, 14(10): 417-419.
    [24] 印丽云, 杨振才, 喻子牛, 等. 海水贝类养殖中的问题及对策[J]. 水产科学, 2012, 31(5): 302-305. doi: 10.3969/j.issn.1003-1111.2012.05.013
    [25] 李亚楠. 贝类疱疹病毒组织亲嗜性及致病性研究[D]. 天津: 天津农学院, 2019: 1-75.
    [26] SHI M, EDWARD C H, ZHANG Y Z, et al. Redefining the invertebrate RNA virosphere[J]. Nature: Int Weekly J Sci, 2016, 540(7634): 539-543.
    [27] ROSANI U, GERDOL M. A bioinformatics approach reveals seven nearly-complete RNA-virus genomes in bivalve RNA-seq data[J]. Virus Res, 2017, 239: 33-42. doi: 10.1016/j.virusres.2016.10.009
    [28] IAN H, JACKSON E W, WILHELM R C, et al. Diversity of sea star-associated densoviruses and transcribed dndogenous viral elements of densovirus origin[J]. J Virol, 2020, 95(1): e01594-20.
    [29] CUI J, ZHANG Y Y, CHEN Y C, et al. Viromes in marine ecosystems reveal remarkable invertebrate RNA virus diversity[J]. Sci China Life Sci, 2021, 64: 1-12.
    [30] 靳泽华, 黄英, 王泽宇, 等. 鸡传染性贫血病毒湖北分离株XH16全基因组序列分析[J]. 中国兽医杂志, 2020, 56(12): 1-8.
    [31] 闫瑞杰. 猪圆环病毒病的危害[J]. 今日畜牧兽医, 2021, 37(7): 19-49. doi: 10.3969/j.issn.1673-4092.2021.07.012
    [32] HUI A, ALTAN E, SLOVIS N, et al. Circovirus in blood of a febrile horse with hepatitis.[J]. Viruses, 2021, 13(5): v13050944.
    [33] BREITBART M, DELWART E, ROSARIO K, et al. ICTV virus taxonomy profile: circoviridae[J]. J Gen Virol, 2017, 98(8): 1997-1998. doi: 10.1099/jgv.0.000871
  • 加载中
图(7) / 表(2)
计量
  • 文章访问数:  162
  • HTML全文浏览量:  14
  • PDF下载量:  5
  • 被引次数: 0
出版历程
  • 收稿日期:  2021-09-09
  • 修回日期:  2021-11-03
  • 网络出版日期:  2021-11-30

目录

    /

    返回文章
    返回