Bousios et al. BMC Genomics 2010, 11:89 http://www.biomedcentral.com/1471-2164/11/89 Sireviruses are the ‘obese’ members of the Pseudoviridae family A comparative analysis of the size between Sireviruses and classic elements revealed that Sireviruses share an exceptionally large genome that clearly differentiates them from other Ty1/copia retrotransposons (Table 2). So far few publications have commented on the length of single Sirevirus elements, the most recent reporting on the large genome of the Maximus lineage [34], ignor- ing however that Maximus belongs to the Sirevirus genus. The average Sirevirus length (10.55 kb) is twice as long as that of classic Ty1/copia elements (5.6 kb). The difference derives from the large LTRs (1.28 kb compared to 0.56 kb), linker domain (1.5 kb to 78 bp), expanded gag (660 to 330 amino acids) and ENV (1.8 kb when present). The sum of the extended regions equals to 5.5 kb and hence matches the size difference. Discussion The novel in silico analysis of the Sirevirus genome and the comparison to a group of representative classic ele- ments provided what we believe are major insights into the structure of LTR retrotransposons. Our data show that Sireviruses form an ancient lineage, at least as old Page 9 of 14 as those of other classic Ty1/copia elements. The main characteristic of their genome is the high sequence divergence of their large non-coding domains, which are however full of highly conserved microdomains in key regions (Figure 6) that indicate participation in every step of the retrotransposon life cycle, from activation to reverse transcription to integration in the new locus. The position and organization of the motifs do not seem coincidental: i) the novel RMs define CpG islands at the ENV 5’ terminus and in the LTRs adjacent to the TATA box, ii) the junctions contain highly conserved PBS, PPT and attachment sites, whilst an IR accurately surrounds the terminal PPT, iii) multiple identical PPTs cluster next to the 3’LTR and iv) the integrase signal occurs at the predicted domain at the 3’ end of the LTRs. These features may be among the underlying fac- tors that contribute towards the Sirevirus distribution in plants. The high conservation of the Sirevirus LTR junctions indicates strict sequence requirements towards reverse transcription and integration The PPT and the pairing of the tRNA molecule to the PBS are used as primers during reverse transcription to initiate Figure 6 The organization of the highly conserved microdomains in the Sirevirus genome. The coloring follows the pattern of previous figures. The conserved 16 mer of the 5’LTR/PBS junction is shown in orange, whilst the integrase signal at the 3’ terminus of the LTRs in light blue. The size difference of Sireviruses and classic retrotransposons is approximately drawn to scale (see also Table 2).