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Endogenous Viral Elements in Animal Genomes

Figure 1

Viral replication strategies, endogenous viral elements, and the genomic fossil record.

Animal viruses exhibit a range of genome types and replication strategies. While all viruses must produce mRNA in order to express proteins, steps between entry into the cell and the expression of mRNA vary greatly. Examples of the known animal virus replication strategies are shown to the left of the figure, with the representative families listed for each case. Arrows indicate steps in replication. Red lines indicate pathways that lead to viral genetic material becoming integrated into the nuclear genome of the host cell. Retroviruses are unique amongst animal viruses in that integration occurs as an obligate step in replication. 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. Abbreviations: dsDNA (double stranded DNA); ssDNA (single stranded DNA, dsRNA (double stranded RNA); RNA-ve (negative sense, single stranded RNA); RNA-ve (negative sense, single stranded RNA); RNA+ve (positive sense, single stranded RNA).

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1001191.g001