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Welcome to DIGS-for-EVEs - collating the viral fossil record!
Endogenous viral elements (EVEs) are fragments of viral DNA that have been integrated into the genome of a host organism through ancient infections. Over evolutionary timescales, these viral sequences have become a permanent part of the host's genetic material, providing a unique window into the interactions between viruses and their hosts over millions of years. The study of EVEs offers valuable insights into viral evolution, host-virus co-evolution, and the long-term impacts of viral infections on the genetic diversity of eukaryotes. Because EVEs preserve information about ancient viruses, they provide a kind of viral fossil record.
The DIGS-for-EVEs repository collates and organizes EVEs found in eukaryotic genomes.
This resource provides a curated catalog of EVE sequences identified from publicly available genome data using the Database-Integrated Genome Screening (DIGS) Tool.
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.
The DIGS-for-EVEs repository includes a collection of utility scripts designed to help researchers interact with the EVE catalog and perform data analysis tasks. These scripts offer functionalities such as:
- Namespace Management: Easily view the used and available namespaces for EVEs to understand their naming conventions.
- Data Querying: Efficiently extract specific information from the catalog based on user-defined criteria.
- Phylogenetic Analysis Tools: Streamline the process of performing phylogenetic analysis on EVE sequences.
Studying EVEs is crucial for understanding the hidden history of viral infections and their impact on host genomes. By analyzing these viral fossils, researchers can uncover:
- Evolutionary Patterns: Insights into how viruses have evolved and adapted to different host species over time.
- Host-Virus Interactions: Evidence of the molecular arms race between viruses and their hosts, shaping immune responses and genetic defenses.
- Genomic Innovations: The role of viral sequences in driving genomic innovation and the emergence of new biological functions in hosts.
DIGS-for-EVEs is an open-ended and collaborative project that continues to evolve as new genomic data and viral discoveries emerge. We welcome contributions from the research community to help expand and refine this resource. To get involved:
- Contribute Data: Submit newly identified EVEs or suggest updates to the existing catalog.
- Collaborate on Research: Reach out to discuss potential research collaborations using the DIGS-for-EVEs resource.
- Report Issues: Help us improve by reporting any issues or inconsistencies you find in the catalog.
As the field of genomics advances, DIGS-for-EVEs will be continuously updated to include the latest data and insights. Stay tuned for updates on newly identified EVEs, revised classifications, and expanded datasets.
DIGS-for-EVEs by Robert J Gifford Lab.
For questions, issues, or feedback, please open an issue on the GitHub repository.