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

doi:10.12131/20210260

新型牡蛎相关圆环病毒基因组的鉴定

doi: 10.12131/20210260

杨李玲^{1, 2,},
郭迎香^{1, 2},
位红颖³,
王萌⁴,
方艺菲⁵,
朱鹏⁶,
姜敬哲^2, ,

1.
天津农学院，天津 300384
2.
中国水产科学研究院南海水产研究所/农业农村部南海渔业资源开发利用重点实验室，广东广州 510300
3.
广州美格基因科技有限公司，广东广州 510005
4.
从化区农业农村局，广东广州 510925
5.
上海美吉生物医药科技有限公司，上海 201321
6.
上海海洋大学，上海 201306

基金项目: 国家自然科学基金面上项目(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(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
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- 文章访问数: 291
- HTML全文浏览量: 45
- PDF下载量: 28
- 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
- 刊出日期: 2022-08-05

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

YANG Liling^{1, 2
,},
GUO Yingxiang^{1, 2},
WEI Hongying³,
WANG Meng⁴,
FANG Yifei⁵,
ZHU Peng⁶,
JIANG Jingzhe^{2
, ,}

1.
Fisheries College, Tianjin Agricultural University, Tianjin 300384, 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.
Guangzhou Mega Gene Technology Co., Ltd., Guangzhou 510005, China
4.
Bureau of Agriculture and Rural Affairs of Conghua District, Guangzhou 510300, China
5.
Shanghai Meiji Biomedical Technology Co., Ltd., Shanghai 201321, China
6.
Shanghai Ocean University, Shanghai 201318, China

摘要

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。
- 圆环病毒 /
- 生物信息分析 /
- 香港牡蛎 /
- 复制酶 /
- 结构域
Abstract: The lack of pathogen genome information is one of the main reasons for the slow progress of oyster disease research. In order to identify more oyster-associated viruses, based on the previously obtained viromic data of oysters (Crassostrea hongkongensis) cultured in multiple locations along the coast of the South China Sea, after quality control, assembly, and species annotation of the sequencing data, we selected the putative circovirus genome sequences for the construction of the phylogenetic tree, genome comparison, protein domain analysis, structure prediction and virus abundance analysis, which provides references for the research of oyster disease. The results show that five viral sequences clustered with known circoviruses in a large branch, indicating that they are members of the Circoviridae family. The five viral genome sequences all contained replication protein genes, with the highest similarity to a replication protein sequence of arthropod circovirus. The five sequences and seven other public database sequences formed an independent sub-branch. Viruses on this branch were mostly from animal-related samples. Based on the domain analysis (SMART), replicase conserved domains were identified in most sequences.
- Circovirus /
- Bioinformatics analysis /
- Crassostrea hongkongensis /
- Replication /
- Domain

HTML全文

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)

下载: 全尺寸图片幻灯片

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

下载: 全尺寸图片幻灯片

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)

下载: 全尺寸图片幻灯片

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

下载: 全尺寸图片幻灯片

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

下载: 全尺寸图片幻灯片

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

下载: 全尺寸图片幻灯片

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

下载: 全尺寸图片幻灯片

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	科 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
样本ID Sample ID	ML2-k141_27933	ZHd1-k141_220676	ML2-k141_11943	T5S3-k141_267932	QZd1-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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