To identify whether our putative viral contigs were expressed endogenous viral elements, we initially searched for disrupted ORFs using Geneious Prime (v.2022.0). Next, we screened for flanking host regions using CheckV and BLASTn. We also searched for flanking long terminal repeats as these are associated with integrated proviruses (Johnson 2019 (link)). Contigs with intact ORFs that were not flanked by host genes or repeats were subsequently used as a query against all vertebrate genomes available on NCBI using tblastn, with an e-value threshold of 1 × 10–20 (Shi et al. 2018 (link)). We used all published vertebrate genomes as no genomes are currently available for the reef fish studied here. Viral sequences identified as endogenous were removed from subsequent analyses.
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Identifying Endogenous Viral Elements
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Corresponding Organization : University of Sydney
Other organizations : James Cook University, University of Otago, Institute of Environmental Science and Research
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Variable analysis
independent variables
- Presence of disrupted ORFs
- Presence of flanking host regions
- Presence of flanking long terminal repeats
- Presence of intact ORFs not flanked by host genes or repeats
- Identification of endogenous viral elements
- Vertebrate genomes available on NCBI
- Positive control: Not specified
- Negative control: Not specified
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