Bousios et al. BMC Genomics 2010, 11:89 http://www.biomedcentral.com/1471-2164/11/89 Sirevirus clade compared to the other retrotransposons are in broad agreement with previous RT phylogenetic analyses [20], suggesting the recent colonization of their host genomes. Intriguingly, despite the closer evolutionary relation- ship than classic elements, the sequence organization of the Sirevirus genome appears to be highly divergent, as much as (or even more than) the genome of classic ret- rotransposons (Figure 1). In fact, excluding the coding domain, the non-coding regions are more diverse in Sir- eviruses (Table 1), which suggests that the mutation rates of genome change are similar or even higher in the Sirevirus genus compared to other Pseudoviridae retrotransposons. Consequently, the RT/RH-derived recent evolutionary origin of Sireviruses may be plas- matic and the genus may in reality represent an ancient lineage. Overall, the average pairwise identity of the full- length genome of Sireviruses and classic elements is equally low (17% and 13% respectively), whilst the Sire- virus linker domain and LTRs are extremely diverse (Table 1). Thus, the highly conserved motifs discussed herein are most likely not the result of general sequence similarity within the Sirevirus genome. Page 3 of 14 Multiple identical PPTs is a unique feature of the Sirevirus linker domain Unsupervised discovery of sequence motifs with the use of the TEIRESIAS pattern discovery algorithm [25] primarily identified the downstream 3’ end of the internal domain as the most conserved area of the Sirevirus genome, which corresponds to the region where the PPT is located. Post- discovery analysis, however, differentiated the area into two discrete sub-regions, the PPT and an IR, that have dif- ferent characteristics. The first motif is the 8 bp 5’- AGGGGGAG-3’ sequence, which is found precisely 10 bp upstream of the 3’LTR of all elements. TEIRESIAS detected many identical PPT copies in the linker of every Sirevirus, irrespective of the length of the domain or the presence of the ENV-gene (Figure 2b and Table 2). On average, four PPTs are found in each linker, preferentially clustered near the 3’LTR junction (83% within 0.5 kb from the 3’LTR). The biased multiple PPT topology is exempli- fied in the ENV-containing Sireviruses, where the vast majority of upstream PPTs (56/63, 89%) reside after the ENV-gene (Table 2). The presence of the PPTs in the lin- ker domain is not coincidental, as the octamer is rarely found in the rest of the Sirevirus genome (0.3/element). Figure 1 Genome diversity of Ty1/copia retrotransposons. Pairwise score identity of the various genomic regions of Sireviruses and classic elements and of the Sirevirus conserved motifs. Classic Ty1/copia elements with linker domain smaller than 25 bp are not included in the respective analysis. Most domains that are shared between the two retrotransposon datasets appear to be equally divergent (see also Table 1). SV, Sirevirus; Cl, Classic elements; Full, full length element; LD, linker domain; GP, gag-pol; PBS, conserved 5’LTR/internal domain junction; PPT, linker domain/3’LTR junction; IntS, integrase signal; TATA, TATA box-like motif.