Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Jan 31;16(2):228.
doi: 10.3390/v16020228.

Unveiling CRESS DNA Virus Diversity in Oysters by Virome

Peng Zhu  1   2   3 , Chang Liu  2   4 , Guang-Feng Liu  2 , Hong Liu  3 , Ke-Ming Xie  2   5 , Hong-Sai Zhang  1   2 , Xin Xu  6 , Jian Xiao  6 , Jing-Zhe Jiang  1   2   5
Affiliations

Unveiling CRESS DNA Virus Diversity in Oysters by Virome

Peng Zhu et al. Viruses. .

Abstract

Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.

Keywords: CRESS DNA virus; Cap; Rep; oyster; phylogenetic tree; virome.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Similarity clustering networks of oyster-associated CRESS DNA virus sequences. (A) Clustering network of 1012 Rep protein sequences. (B) Clustering network of 827 capsid protein sequences. The networks were visualized using the Fruchterman–Reingold algorithm in Gephi (version 0.9.2). Dots represent different proteins. Edges indicate that the DIAMOND BLASTP scores ≥ 150 (A) and ≥42.7 (B) between the connected dots.
Figure 2
Figure 2
Maximum likelihood phylogenetic tree of CRESS5 and oyster-related viruses. The maximum likelihood phylogenetic tree was constructed using IQtree (version 2.1.4) based on the Rep (A) and Cap (B) amino acid sequences of CRESS5. ModelFinder was set to MFP, and 1000 ultrafast bootstraps were used. Bootstrap values > 70 are shown. The color of the line corresponds to the color of the virus source shown. Extensive recombination can be inferred when replicase proteins are associated with coat proteins and with different types of structural proteins and vice versa.
Figure 3
Figure 3
Maximum likelihood phylogenetic tree (A,C) and genome structure (B) of Smacoviridae and oyster-related viruses. The maximum likelihood phylogenetic tree was constructed using IQtree (version 2.1.4) based on the Rep amino acid sequences of Smacoviridae-like viruses. ModelFinder was set to MFP, and 1000 ultrafast bootstraps were used. Bootstrap values > 70 are shown. The color of the line corresponds to the color of the virus source shown. Extensive recombination can be inferred when replicase proteins are associated with coat proteins and with different types of structural proteins and vice versa. Genome structure was used for SnapGene (version 4.3.6).
Figure 4
Figure 4
Maximum likelihood phylogenetic tree of oyster-related Cirlivirales. The maximum likelihood phylogenetic tree was constructed using IQtree (version 2.1.4) based on the Rep (A) and Cap (B) amino acid sequences of CRESS DNA viruses. ModelFinder was set to MFP, and 1000 ultrafast bootstraps were used. Bootstrap values > 70 are shown. The color of the line corresponds to the color of the virus source shown. Extensive recombination can be inferred when replicase proteins are associated with capsid proteins and with different types of structural proteins and vice versa.
Figure 5
Figure 5
Maximum likelihood phylogenetic tree of CRESS-Rec1 and oyster-related virus. The maximum likelihood phylogenetic tree was constructed using IQtree (version 2.1.4) based on the Rep amino acid sequences of CRESS-Rec1. ModelFinder was set to MFP, and 1000 ultrafast bootstraps were used. Bootstrap values > 70 are shown.
Figure 6
Figure 6
Genetic exchange among CRESS DNA Viruses. Comparison of the phylogenetic trees of replicase-associated proteins (A) and capsid proteins (B) from four different clusters. ①, ②, ③, and ④ in (A) correspond to the four Clusters in Supplementary Figure S2A. And ①, ②, ③, and ④ in (B) correspond to the four Clusters in Supplementary Figure S2B. The color of the line corresponds to the color of the virus source shown. Widespread recombination can be inferred when Rep clades are associated with different types of structural protein and vice versa.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Powell D., Subramanian S., Suwansa-ard S., Zhao M., O’Connor W., Raftos D., Elizur A. The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves. DNA Res. 2018;25:655–665. doi: 10.1093/dnares/dsy032. - DOI - PMC - PubMed
    1. Olalemi A., Baker-Austin C., Ebdon J., Taylor H. Bioaccumulation and persistence of faecal bacterial and viral indicators in Mytilus edulis and Crassostrea gigas. Int. J. Hyg. Environ. Health. 2016;219:592–598. doi: 10.1016/j.ijheh.2016.06.002. - DOI - PubMed
    1. Zhang G., Fang X., Guo X., Li L., Luo R., Xu F., Yang P., Zhang L., Wang X., Qi H., et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature. 2012;490:49–54. doi: 10.1038/nature11413. - DOI - PubMed
    1. Li J., Zhang Y., Zhang Y., Mao F., Xiang Z., Xiao S., Ma H., Yu Z. The first invertebrate NFIL3 transcription factor with role in immune defense identified from the Hong Kong oyster, Crassostrea hongkongensis. Dev. Comp. Immunol. 2017;76:1–8. doi: 10.1016/j.dci.2017.05.011. - DOI - PubMed
    1. Farley C.A., Banfield W.G., Kasnic G., Jr., Foster W.S. Oyster herpes-type virus. Science. 1972;178:759–760. doi: 10.1126/science.178.4062.759. - DOI - PubMed