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Endogenous viral elements (EVEs) are viral DNA fragments that have become permanently integrated into the genomes of host organisms as a result of ancient viral infections, and are inherited across generations. Many of these sequences are millions of years old, and these ancient viral remnants effectively serve as a viral “fossil record” preserving invaluable information about past viral lineages and their historical interactions with hosts. Studying EVEs sheds light on viral evolution, host-virus co-evolution, and the long-term influence of viral infections on the genetic diversity of eukaryotes.
The DIGS-for-EVEs repository offers a meticulously curated catalog of EVE sequences identified from publicly available genomic data, using the Database-Integrated Genome Screening (DIGS) Tool.
By providing organized, accessible data, DIGS-for-EVEs aims to support research into the evolutionary history of viruses and their lasting genetic impact on their hosts.
DIGS-for-EVEs aims to make the viral fossil record more accessible to researchers by:
- Creating a Comprehensive EVE Catalog: Organizing EVE sequences into a systematic and searchable database, complete with detailed annotations and metadata.
- Standardizing EVE Nomenclature: Applying a consistent naming convention to ensure that each EVE can be accurately identified and compared across different species and research contexts.
- Facilitating Comparative Genomic Analysis: Providing tools and resources to support the study of orthologous and paralogous relationships among EVEs in different species.
- Systematic Identification: EVEs in this catalog were identified using Database-Integrated Genome Screening (DIGS), a high-throughput computational approach that can be used to systematically screen WGS data for viral sequences, capturing hits in a relational database.
- Curated Annotations: Each EVE is annotated with information about its viral origin, host species, genomic location, and evolutionary relationships.
- Phylogenetic Analysis: In-depth phylogenetic investigations were conducted to classify EVEs into appropriate virus taxonomic groups and to reveal their evolutionary history.
- Ortholog Detection: Comparative genomic analysis was performed to identify orthologous EVE loci in different species, enhancing our understanding of their evolutionary significance.
Researchers and scientists can use the DIGS-for-EVEs catalog as a reference resource to:
- Explore EVE Sequences: Search and browse the catalog to find specific EVEs and examine their annotations, genomic locations, and evolutionary relationships.
- Analyze Viral Evolution: Utilize the catalog's phylogenetic data to study the origins and diversification of viral lineages in host genomes.
- Identify Novel EVEs: Access tools and scripts that can aid in the discovery of new EVE sequences in previously unexamined genome data.
DIGS-for-EVEs by Robert J Gifford Lab.
For questions, issues, or feedback, please open an issue on the GitHub repository.