EVE Project Background - giffordlabcvr/Parvovirus-GLUE GitHub Wiki

Endogenous Parvoviruses

Whole genome sequencing has uncovered DNA sequences derived from parvoviruses within the genomes of vertebrates. These sequences, known as 'endogenous parvoviral elements' (EPVs), are believed to have originated through 'germline incorporation' events, where parvovirus DNA integrated into the chromosomal DNA of germline cells and was subsequently inherited as part of the host's genome.

EPVs offer a unique window into the long-term interactions between parvoviruses and their vertebrate hosts. They provide insights into evolutionary processes, viral discovery, and the role of viral elements in host genomics. The key areas of interest when studying EPVs include:

  • Evolution: EPVs reveal important information about the evolutionary history of parvoviruses, shaping our understanding of their biology and how they have co-evolved with hosts over millions of years.

  • Genomics: Some EPVs may have had functional roles as host alleles, influencing the evolution of the host genome. The prevalence of multicopy EPV lineages in certain species suggests that the germline incorporation of parvovirus sequences could have had significant evolutionary impacts.

  • Virus discovery: Including EPVs in phylogenetic analyses when identifying new parvovirus species provides important context. Additionally, EPV sequences help exclude potential 'false positives' in metagenomics-driven virus discovery efforts, where sequences that seem to represent novel parvoviruses might actually derive from the host's genomic DNA.

  • EVE discovery: EPV sequences can serve as 'probes' for in silico genome screening, aiding in the discovery of novel endogenous viral elements.

What the Parvovirus-GLUE EVE Extension Offers:

The Parvovirus-GLUE-EVE project is a comprehensive and user-friendly resource for analyzing EPV sequences. Key features include:

  • GLUE Framework Integration: As part of the Parvovirus-GLUE project, all EPV information can be accessed via GLUE's command layer, eliminating the need for time-consuming pre-processing and enabling streamlined workflows.

  • Standardized Nomenclature: A well-structured naming system for EPV loci ensures clarity and facilitates interoperability across studies.

  • Genomic Mapping: Detailed maps of the precise genomic locations of all known EPV loci in published whole genome sequences, including flanking upstream and downstream genes. Where orthology permits, minimum age estimates for EPVs are provided, along with alignments of orthologous sequences.

  • Paleovirus Consensus Genomes: Annotated consensus genomes reconstruct the ancient parvoviruses that gave rise to EPVs, offering a glimpse into these viral ancestors.

  • Sequence Alignments: Pre-aligned EPV sequences alongside modern parvovirus genomes to aid in comparative analyses.

  • Evolutionary Phylogenies: Phylogenetic trees that illustrate the evolutionary relationships between EPV sequences and extant parvoviruses, shedding light on the long-term co-evolution of parvoviruses with their hosts.