Speaker
Description
Endogenous Viral Elements (EVEs) originate when viruses integrate their genetic material into the host genome, becoming a permanent part of the host’s DNA. As molecular fossils of ancient viral infections, EVEs offer valuable insights into host-virus coevolution and virus diversity over evolutionary timescales.
We aim to detect EVEs across 948 mammalian genomes by performing a nested homology search of virus proteins within host genomes using DIAMOND. Our search begins by identifying potential EVE candidates with a query of 175,440 virus proteins. We refine these candidates throug reciprocal searches against the non-redundant protein database and a clustered version of the reference viral database (RVDB) from NCBI. Finally, we attempt to reconstruct ancestral proteins using GeneWise.
The complex co-evolutionary history between viruses and hosts derives into a constant genetic exchange, resulting not only in viral sequences in host genomes, but also host-derive proteins co-opted by viruses — false positive results that do not represent true endogenization events. Additionally, our searches yield an overwhelming amount of data. For example, in primates alone, we obtained 2, 510, 280 EVE candidates longer than 100 amino acids that require further classification.
To interpret our results, we propose a network-based approach where nodes represent clusters of similar proteins, and edges connect proteins based on genomic proximity. We will explore whether within-cluster statistics, such as species diversity or sequence length, and network-based metrics like edge degree or centrality transitivity can effectively classify EVE candidates. We speculate that such metrics may be useful for distinguishing the different types of sequences in our results, including virus-co-opted proteins, EVEs, and other genetic elements such as actively expressed retroviruses or retrotransposable elements. With this work, we intend to expand the methods used to study these ancient genetic elements and improve our understanding of the role of viruses in shaping the evolution of host genomes.
| Expedited Notification | No thanks, I do not require Expedited Notification |
|---|
