Aris Katzourakis; Robert J. Gifford

“ EVEs related to rhabdoviruses were identified in the black-legged tick genome (Ixodes scapularis) , and in the genomes of both Aedes and Culex mosquitoes. Among these were insertions that encoded intact NP and GP ORFs (Figure 2a) . Phylogenies constructed using NP tentatively grouped rhabdovirus EVEs derived from mosquitoes in a clade with lyssaviruses and Drosophila sigma virus (Figure 2d) . However phylogenetic support for this clade was very weak, with only 20% bootstrap support for the monophyly of the clade, although support for the grouping of EVEs from Aedes and Culex was high (96%) . ”

“ Importantly, the rate at which EVEs are exapted as restriction factors in animals could greatly exceed their rate of fixation in animal genomes.
The diverse EVE sequences described in this report demonstrate an extensive history of gene flow from virus to animal genomes. Animal genomes are a living document of virus and host interaction, and genomic studies have an important role to play in advancing understanding of virus and host evolution. ”

“ For all other animal viruses integration occurs anomalously, through interaction with cellular retroelements such as LINEs, or via non-homologous recombination with genomic DNA. If integration occurs in a germ line cell that goes on to develop into a viable host organism, an EVE is formed. ”

“ Green lines show the evolution of an EVE in its host lineage. In the example given, the EVE reaches genetic fixation at the point indicated, and is inherited by all descendant hosts thereafter. Assuming that insertion occurs randomly, the presence of related EVEs at the same locus in both descendant species A and B indicates that insertion occurred prior to their divergence, allowing a minimum age for the insertion to be inferred from the estimated timescale of their evolution. Conversely, the presence of an empty insertion site in species C provides a maximum age for the insertion. ”

“ A robust clade (100% bootstrap support) placed four Ixodes EVEs into a single group, suggesting they are likely derived from the same exogenous virus lineage, but their placement relative to other Rhabdoviruses was ambiguous, as they formed a clade with a number of distinct Rhabdoviruses with minimal bootstrap support (8%) . Phylogenies constructed using L-polymerase sequences weakly grouped Ixodes and Aedes insertions with Lyssaviruses and Moussa virus, but not Drosophila sigma virus. ”

“ Evolution of EBLN elements in primates. (a) The primate clade marked by an asterisk in the phylogeny shown in Figure 6 is shown in greater detail here, with the number of stop codons in the EBLN-1 locus indicated for seven species. Orthology across these species indicates that EBLN-1 predates the divergence of these species 54 million years ago [35] . Monte Carlo simulations in which a consensus EBLN sequence was allowed to neutrally evolve at the primate neutral rate for this length of time showed that the average number of stop codons expected after this time is fifteen. ”

“ The majority of parvovirus EVEs were not intact, and are unlikely to express RNA or protein. However, a dependovirus EVE in the genome of the African elephant (Loxodonta africana) encoded an intact NS1 gene (Figure 5a) . Additionally, screening of EST databases identified expressed sequences related to an opossum parvovirus EVE in another marsupial species - the brush tailed possum (Trichosurus vulpecula) .
Adeno-associated virus 2 (AAV-2) integrates at a specific site in human chromosome 19 [33] , [34] . ”

“ 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. ”

“ EVEs derived from different genes never occurred as contiguous sequences, and consequently we could not determine whether EVEs derived from distinct genes of a given virus family originated from the same or distinct virus lineages/infections.
Table 1 "Distribution and diversity of EVEs identified by in silico screening. (10.1371/journal.pgen.1001191.t001) " Footnote: Groups that have been reported as mediating their own integration are highlighted in bold. Asterisks denote families with representatives known to be capable of establishing persistent/latent infection. ”

“ Phylogenetic relationships of dependovirus EVEs and representative exogenous viruses, based on NS1 gene and rooted on snake parvovirus. A dolphin EVE (indicated by an asterisk) groups robustly with avian rather than mammalian isolates. (d) Phylogenetic relationships of parvovirus EVEs and representative exogenous viruses, based on NS1 gene and rooted on Aleutian mink disease virus. Support for both ML phylogenetic trees was evaluated using 1,000 nonparametric bootstrap replicates. EVEs potentially comprising a new genus are indicated. ”

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