Project Scope

Focus and Limitations

The DIGS-for-EVEs project focuses on the systematic identification and annotation of endogenous viral elements (EVEs) derived from viruses with genome sizes under 30 kilobases. This criterion was chosen to concentrate on virus groups that are most amenable to in silico screening and to minimize the complexity associated with larger viral genomes.

• Viruses Included: The project targets RNA viruses, single-stranded DNA (ssDNA) viruses, and other small genome viruses that integrate into host genomes. These viruses often leave behind traces in the form of EVEs, which can be identified and analyzed using computational methods.

• Viruses Excluded: Large genome viruses, such as poxviruses and other large double-stranded DNA (dsDNA) viruses, are currently excluded from the scope of this project due to their genome size exceeding 30 kilobases. The complexity of these larger viral genomes makes them less tractable for the high-throughput analysis methods employed in this study.

• Host Species Included: So far the project has focussed on multicellular eukaryotes. Only data from vertebrate animals have been published at this point.

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Evolution of the Project Scope

The scope of DIGS-for-EVEs is expected to evolve as the field of genomics advances and new data become available. Several factors contribute to this open-ended nature:

1. Continuous Data Accumulation:

   • As new genome assemblies are published, they offer fresh opportunities to identify novel EVEs that were not previously detectable.
   • The project's dataset will be continuously updated to incorporate these new findings, expanding our understanding of viral integration across different host species.

2. Discovery of Novel Viruses:

   • The identification of new viral species or lineages can lead to the discovery of previously unknown EVEs.
   • By continually integrating data on novel viruses, DIGS-for-EVEs remains a dynamic resource that reflects the most up-to-date knowledge of viral evolution and host-virus interactions.

3. Challenges in EVE Identification:

   • Discriminating EVEs from other types of genomic sequences can be straightforward for some virus groups but challenging for others.
   • The project initially focuses on the most tractable types of EVEs to establish a robust foundation, with plans to expand into more complex virus groups as the methodology evolves.

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Strategy for Expansion

The project's expansion strategy involves a phased approach to broaden the range of virus groups and host species studied. Our goal is to cover the widest possible range of eukaryotic hosts while prioritizing the most accessible and scientifically valuable data. Over time, we plan to:

• Extend the analysis to include virus groups with moderately larger genomes as new computational tools and methodologies become available.
• Refine the criteria for identifying EVEs to improve accuracy in distinguishing them from other genomic elements, such as transposons and host gene sequences.
• Increase the taxonomic breadth of the host species included in the study, incorporating more diverse groups of eukaryotes.

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Future Directions

DIGS-for-EVEs is designed as a long-term project with the flexibility to adapt to the changing landscape of viral and genomic research. Our focus will continue to be on providing a comprehensive and organized collection of EVE data that serves as a valuable resource for researchers studying viral evolution, host-virus co-evolution, and the impact of ancient viral infections on modern genomes.

• Open-ended Research: The project's adaptability allows for incremental updates as new insights are gained from both experimental studies and computational advances.
• Community Contributions: We welcome contributions from researchers around the world to help expand and refine the dataset. Collaboration is encouraged to ensure that the resource remains relevant and up-to-date.

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