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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 new type of oyster-related circovirus genome Comparative 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 new type of oyster-related circovirus genome Comparative 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 new type of oyster-related circovirus genome Comparative 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一个主要原因。为鉴定更多牡蛎相关病毒,该研究基于前期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,说明其是圆环病毒科成员;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)

    其中红色五角星标识为本研究中候选的5条基因组序列,基因组树中内圈颜色表示病毒科,外圈颜色表示病毒宿主来源。

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

    Red stars represent the five candidate viral genomes in this study. The color of the inner circle represents virus families in the genome tree, and the color of the outer circle represents different viral hosts.

    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

    使用MAFFT进行基因组序列比对,trimAI对齐氨基酸序列,MEGA建树并可视化,Neighbor-joining Tree;Bootstrap Replications: 1 000; substitution model: p-distance。

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

    After aligning genome sequences with MAFFT, amino acid sequences were aligned with trimAL and visualized with MEGA. Neighbor-joining tree; Bootstrap Replications: 1 000; substitution model: p-distance.

    图  3  圆环病毒基因组序列间的ANI (Average nucleotide identity, a) 和复制酶蛋白序列间的AAI (Amino acid identity,b) 圆圈直径和着色深浅代表ANI值和AAI的大小。

    Figure  3.  ANI value among genomic sequences (a) and AAI value among replication proteins of circoviruses (b) The circle diameter and color depth represent the value of the ANI and AAI.

    图  4  牡蛎相关圆环病毒比较基因组分析图

    5张图中上面的序列均为NC_017843.2,下面序列为本研究中候选5条圆环病毒基因组序列。

    图  5  牡蛎相关圆环病毒复制酶蛋白进化树

    MAFFT比对氨基酸序列,trimAL序列对齐,用MEGA建树并可视化,Neighbor-joining Tree; Bootstrap Replications: 1 000; substitution model: p-distance; Site Coverage Cutoff: 50%.其中红色为本研究中候选的5条基因组序列,黄色代表来源于动物宏基因组,蓝色是海洋病毒,绿色代表其他。

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

    After aligning amino acid sequences with MAFFT, amino acid sequences were aligned with trimAL and visualized with MEGA. Neighbor-joining tree; Bootstrap Replications: 1 000; substitution model: p-distance; Site Coverage Cutoff: 50%. Red represents the five candidate genome sequences in this study, yellow represents the animal metagenomic, blue represents the marine virus, and the green represents the others.

    图  6  牡蛎相关圆环病毒复制酶蛋白序列比对

    其中7条序列分别为5条候选病毒和参考蛋白ARI44308.1、YP_006281010.1。

    Figure  6.  Sequence alignment of oyster-related circoviruses

    The seven sequences were five candidate viruses and reference proteins ARI44308.1 and YP_006281010.1, respectively.

    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ORF位置
    Location of replication protein ORF
    衣壳蛋白ORF位置
    Location of capsid protein ORF
    ML2-k141_11943圆环病毒科2 2811~7441 015~1 968
    ML2-k141_27933圆环病毒科2 170335~1 1021 338~1 946
    QZd1-k141_2132圆环病毒科1 942179~9761 303~1 941
    T5S3-k141_267932圆环病毒科2 1371~816951~1 841
    ZHd1-k141_220676圆环病毒科1 938659~1 5673~503
    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 The 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
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  • 文章访问数:  63
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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

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