Identification of a novel oyster-related circovirus genome compa-rative genome analysis of oyster-related circoviruses
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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。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.
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Key words:
- Circovirus /
- Bioinformatics analysis /
- Crassostrea hongkongensis /
- Replication /
- Domain
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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 ORFML2-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 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_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 -
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