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Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs) derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.

Original publication

DOI

10.1371/journal.pgen.1001191

Type

Journal article

Journal

PLoS Genet

Publication Date

18/11/2010

Volume

6

Keywords

Animals, Base Sequence, Computational Biology, DNA Viruses, Fossils, Gene Flow, Genes, Viral, Genetic Variation, Genome, Mutagenesis, Insertional, Open Reading Frames, Phylogeny, Primates, RNA Viruses, Virus Replication