Exploring the double-stranded DNA viral landscape in eukaryotic genomes
Zhao, H.; Meng, L.; Zhang, R.; Gaia, M.; Ogata, H.
Show abstract
Sequences of viral origin constitute a large proportion of the genomes of certain eukaryotes, yet the role of double-stranded (ds)DNA viruses in shaping the genomes of diverse eukaryotes remains underexplored. Here, we present a computational framework to identify dsDNA viral regions (VRs) in eukaryotic genomes, which was we used to screen 37,254 eukaryotic genome assemblies. In total, 781,111 VRs were identified across 7,103 (19%) assemblies. VRs were found to occupy 16% of a bivalve genome assembly and over 10% of diverse invertebrate and protist genomes. These VRs recovered 29 of the 43 class-level virus-eukaryote associations previously established by virus isolation, and additionally indicated 144 candidate associations for which virus isolation evidence is currently lacking. Some VRs form previously unrecognized deep viral clades, whereas others are phylogenetically related to known viruses. Our study provides a baseline for the extent to which dsDNA viral elements are embedded in diverse eukaryotic genomes and offers an overview of the endogenous dsDNA virosphere. The resulting catalog of viral genomic elements offers opportunities for wider exploration of the significance of virus-host coevolutionary processes.
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