Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals

Abstract

The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host-parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. Endogenous retroviruses (ERVs), however, integrate into the germline of their hosts, and are subjected to their evolutionary rates. This study describes, for the first time, a retroviral orthologue predating the divergence of placental mammals, giving it a minimum age of 104-110 Myr. Simultaneously, other orthologous selfish genetic elements (SGEs), inserted into the ERV sequence, provide evidence for the oldest individual mammalian-wide interspersed repeat and medium-reiteration frequency interspersed repeat mammalian repeats, with the same minimum age. The combined use of shared SGEs and reconstruction of viral orthologies defines new limits and increases maximum 'lookback' times, with subsequent implications for the field of paleovirology.

Keywords: genomics; mammalian evolution; mammalian-wide interspersed repeat; paleovirology; retrovirus evolution; selfish genetic elements.

Figure 1.

ERV-L integration site: (a) 5′ integration site, showing the extreme end of the 5′ LTR of the ERV-L insertion in 10 mammalian species, together with flanking sequence. (b) Corresponding 30 integration site, showing the extreme end of the 3′ LTR, together with flanking sequence. A conservation colour gradient beneath the nucleotides indicates the level of sequence homology across all 10 mammals, with red showing highest conservation. Triangular flags indicate segments of DNA deleted from a particular species for illustration purposes. Because alignment was poor at these regions, the golden mole was omitted (full flanking region alignments are given in the electronic supplementary material).

Figure 2.

Schematic of ERV-L element and identified repeats: SGEs, identified by RepeatMasker, are individually flagged, with the repeat families being colour-coded. A solo-LTR, present only in the Afrotheria, is highlighted in beige, whereas a region of low homology in the same mammalian superorder is shaded light green. The presence of nucleotide sequence is indicated by horizontal black lines, to make obvious where gaps have been inserted in order to maintain the alignment. Sequence conservation is indicated by a histogram running underneath the alignment. Region 1 and region 2 are demarcated by dark lines running above the alignment, and correspond to the regions used for phylogenetic analysis (region 1 corresponds to figure 5; region 2 corresponds to a second cophylogeny given in the electronic supplementary material).

Figure 3.

Orthologous MIR3 retrotransposon: an MIR3 retrotransposon, and flanking DNA, shared across all 11 mammalian species. The nucleotide sequence beneath each annotation is shown, with a graph running beneath the alignment to indicate site-specific sequence conservation across the taxa.

Figure 4.

Orthologous MER3 DNA transposon: a non-autonomous MER3 hAT-Charlie DNA transposon, and flanking DNA, shared across all 11 mammals. The nucleotide sequence beneath each annotation is shown, with a graph to indicate site-specific sequence conservation across the taxa. Flags indicate deletions that were made for illustrative purposes, in regions that contained unique insertions.

Figure 5.

Retroviral-mammalian cophylogeny: cophylogeny comprising an unrooted maximum-likelihood phylogenetic tree constructed from the described ERV-L element (a) and an adapted schematic rooted mammalian phylogeny (b) [–34]. Species falling into each of the four mammalian superorders are bracketed in blue, while the Afrotherian and Boreoeutherian clades are indicated in red; primates and Sirenia are indicated in beige. Branch lengths on the retroviral tree (a) are scaled to indicate the number of substitutions per site, and bootstrap values are shown. The initial divergence of the placental mammals into Afrotheria and Boreoeutheria is indicated in a box [31,36].

Figure 6.

Syntenic relationship between human chromosome 17 and three selected mammals: a chromosome synteny map adapted from ENSEMBL's SyntenyView, showing syntenic blocks (shaded green) shared between human chromosome 17, where the ERV-L insertion occurs (highlighted in red), and corresponding chromosomes in the horse, pig and chimpanzee. Syntenic blocks containing the ERV-L insertion are shaded pink.