Virus Evolution, 2016, 2(2): vew032 doi: 10.1093/ve/vew032 Research article Foamy-like endogenous retroviruses are extensive and abundant in teleosts Ryan Ruboyianes1,* and Michael Worobey1,* 1Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St., Tucson, AZ 85721, USA *Corresponding authors: E-mail:
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[email protected] Abstract Recent discoveries indicate that the foamy virus (FV) (Spumavirus) ancestor may have been among the first retroviruses to appear during the evolution of vertebrates, demonstrated by foamy endogenous retroviruses present within deeply diver- gent hosts including mammals, coelacanth, and ray-finned fish. If they indeed existed in ancient marine environments hundreds of millions of years ago, significant undiscovered diversity of foamy-like endogenous retroviruses might be pre- sent in fish genomes. By screening published genomes and by applying PCR-based assays of preserved tissues, we discov- ered 23 novel foamy-like elements in teleost hosts. These viruses form a robust, reciprocally monophyletic sister clade with sarcopterygian host FV, with class III mammal endogenous retroviruses being the sister group to both clades. Some of these foamy-like retroviruses have larger genomes than any known retrovirus, exogenous or endogenous, due to unusually long gag-like genes and numerous accessory genes. The presence of genetic features conserved between mammalian FV and these novel retroviruses attests to a foamy-like replication biology conserved for hundreds of millions of years. We estimate that some of these viruses integrated recently into host genomes; exogenous forms of these viruses may still circulate. Key words: paleovirology, endogenous retrovirus, foamy virus, fish, phylogeny.