Quantitative assessment of nucleocytoplasmic large DNA virus and host interactions predicted by co-occurrence analyses
Meng, L.; Endo, H.; Blanc-Mathieu, R.; Chaffron, S.; Hernández-Velázquez, R.; Kaneko, H.; Ogata, H. (2021). Quantitative assessment of nucleocytoplasmic large DNA virus and host interactions predicted by co-occurrence analyses. mSphere 6(2): e01298-20. https://dx.doi.org/10.1128/mSphere.01298-20
In: mSphere. American Society for Microbiology: Washington. e-ISSN 2379-5042, more
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| Author keywords |
NCLDV; Tara Oceans; assessment; co-occurrence; host prediction |
| Authors | | Top |
- Meng, L.
- Endo, H.
- Blanc-Mathieu, R.
- Chaffron, S.
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- Hernández-Velázquez, R.
- Kaneko, H.
- Ogata, H.
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| Abstract |
Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments. |
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