Paleovirus Background - giffordlabcvr/Parvovirus-GLUE GitHub Wiki

Endogenous Parvoviruses

Whole genome sequencing has revealed that DNA sequences derived from parvoviruses are present within vertebrate genomes. These ‘endogenous parvoviral elements’ (EPVs) are thought to have originated via ‘germline incorporation’ events in which parvovirus DNA sequences were integrated into chromosomal DNA of germline cells and subsequently inherited as novel host alleles.

  • Evolution: EVEs provide insights into the long-term evolutionary history of virus groups, which greatly influences how we understand their biology.

  • Genomics: Some EPVs may have, or have had, functional roles as host alleles. The prevalence of multicopy EPV lineages in some species suggests that germline incorporation of parvovirus sequences might have significantly influenced the evolution of host genomes.

  • Virus discovery: When new parvovirus species are identified, inclusion of EVEs in phylogenetic analyses can provide useful contextual information. Addionally, the EPV sequences collated here can be used to exclude any potential 'false positive' hits that arise in metagenomics-driven virus discovery efforts (i.e. sequences that seem to represent new parvoviruses but in fact derive from genomic DNA).

  • EVE discovery: Using the EPV sequences provided here as 'probes' for in silico genome screening may enable the detection of novel EPV elements.

What the Parvovirus-GLUE EVE Extension Offers:

The Parvovirus-GLUE-EVE project is designed to provide a comprehensive and accessible resource for the analysis of EPV sequences. Key features include:

  • GLUE Framework Integration: As part of the Parvovirus-GLUE project, the information contained in this repository can be accessed via GLUE's command layer, minimizing the need for labor-intensive pre-processing and enabling streamlined workflows.

  • Standardized Nomenclature: A structured naming system for EPV loci to ensure clarity and interoperability across studies.

  • Genomic Mapping: A detailed map showing the precise genomic locations of all known EPV loci in published whole genome sequence assemblies, aiding in comparative genomic studies. We include upstream and downstream flanking genes. Additionally, where ortholog allows minimum age estimation we provide these dates, as well as alignments of orthologs.

  • Paleovirus Consensus Genomes: Annotated consensus genomes for the ancient parvoviruses that gave rise to the EPVs, offering a reconstructed view of these viral ancestors.

  • Sequence Alignments: Pre-aligned EPV sequences and modern parvovirus genomes to facilitate comparative analysis.

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