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DIGS for EVEs

Database-integrated genome screening (DIGS) for endogenous viral elements (EVEs)

- GitHub + User Guide + GitHub Download - - Twitter - DIGS Tool + Twitter + DIGS Tool
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WGS assemblies screened in this project were obtained from the NCBI Genome resource.

DIGS was performed using the DIGS tool, an open software framework available here.

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- - Directory Structure -

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The DIGS-for-EVEs repository is organized to categorize EVE loci based on host species groups, virus subdivisions, and catalog version, as follows:

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-	DIGS-for-EVEs/
-	└── eve/
-		└── animals/
-			└── vertebrates/
-				└── nonretroviral/
-					└── version-1.0/
-						├── input/
-						└── output/
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- - Subdirectories -

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- - Detailed Contents -

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- - input/ Directory -

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- - output/ Directory -

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- - Standardised Nomenclature for EVE loci -

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In DIGS-for-EVEs we have applied a systematic approach to naming of non-retroviral EVEs, following a previously developed convention. Each element is assigned a unique identifier (ID) constructed from three components, separated by hyphens:

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e.g. EBLG-Carbovirus.2-Boreoeutheria

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This systematic naming approach facilitates clear identification and comparison of EVEs across different species and research contexts.

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Please note the following:

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  1. EVEs were assigned to virus taxonomic groups as accurately as possible based on phylogenetic/genomic analysis. For EVEs that could not be confidently assigned to a subgroup, the lowest taxonomic rank possible for the EVE type is given (i.e. family).
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  2. We grouped sets of orthologous EVEs using shared numeric IDs. However, some orthologous relationships might have been missed, and some EVEs may have been incorrectly grouped as orthologs when they are actually distinct, paralogous loci. The 'digs_results' table includes information on how well each locus matched its assigned ortholog group via BLAST, providing a way to assess the confidence in these orthology designations.
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  3. When EVEs occur in a single species, the corresponding Latin binomial species name is provided. When EVEs occur as orthologs in multiple species, we provide the taxonomic name of the species group. If the species set corresponds to an unranked clade, we use the name of the closest named group at a lower rank and add the abbreviation 'UR' (unranked) to indicate that no named clade perfectly captures the range of species in which the EVE is found.
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  4. Although the naming convention used here was originally developed for ERVs, we have not yet applied it to ERV loci recovered via DIGS. Given the vast number of ERV loci present in vertebrate genomes, this will inevitably pose more significant challenges and require a longer-term effort compared to non-retroviral EVEs.
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- - Glossary of EVE Types: -

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- - DNA viruses & Retroviruses -

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- - RNA viruses -

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For more information please see the Project Documentation.