Bousios et al. BMC Genomics 2010, 11:89 http://www.biomedcentral.com/1471-2164/11/89 Table 1 Average pairwise score identity (%) of the various domains of Sirevirus (SV) and classic (Cl) elements, and also of the Sirevirus conserved motifs Full length SV - Cl LTR SV - Cl Linker domain SV - Cl† gag/pol SV - Cl 5’LTR/PBS junction SV PPT/3’LTR junction SV Integrase signal SV TATA box SV 16.6 - 13.2 3.9 - 10.5 4.8 - 28.5 34.1 - 16.1 92.7 95.7 88.2 76.2 † Classic Ty1/copia with linker domain smaller than 25 bp are not included in the respective analysis. We searched for variants of the 8 bp motif with no signifi- cant results, which suggests that sequence integrity is essential and under selection. ToRTL1 and Tnd-1 are the only two Sireviruses that show variation in their PPT nucleotide composition compared to the consensus octa- mer. Nevertheless, both elements have the terminal G replaced by an A in all their PPTs, which also points towards strong selective pressure instead of random sub- stitutions within the motif. Conversely to Sireviruses, TEIRESIAS did not discover any conserved motifs in the linker domain and 3’LTR of Page 4 of 14 classic retrotransposons. All elements have a single terminal PPT with a wide range of sequence variation, which does however often resemble the Sirevirus PPT (Figure 2c and Figure 3). Three elements share the Sire- virus octamer, while 17 differ only in one nucleotide. The most common substitutions are the conversions of the G of the 3rd position to a T and the A of the 7th position to a C. A highly conserved attachment site defines the Sirevirus terminal PPT The attachment site consists of a short sequence, usually a di- or trinucleotide, between the PPT and the 3’LTR, and the first few bases, especially the universal dinucleotide TG, of the start of the 3’LTR. It is recognized and pro- cessed by INT during the successful insertion of the new copy into the host genome [26]. TEIRESIAS led us to observe that in the Sirevirus 3’LTR junction the conserved motif includes not only the PPT octamer, but also the fol- lowing four bases. In 20 elements the terminal PPT is fol- lowed by the intervening dinucleotide AT, whilst the universal TG indicates the beginning of the 3’LTR, thus generating the Sirevirus 5’-AT/TG-3’ attachment site (Fig- ure 2b). The overall nucleotide identity of the combined twelvemer is 95.7%. Interestingly, the sequence following Table 2 Analysis of the Sirevirus genome size, the position and number of PPTs Full/Linker/LTR length (kb) † PPTs after ENV PPTs in linker domain † For elements that contain the ENV-gene, the linker domain length was calculated by combining the segments before and after the ENV-ORF. †† The 5’LTR of Tnd-1 is incomplete and therefore the full length is calculated based on the 3’LTR. PPTs before ENV — 1 — 1 — — — — — — 1 1 — 3 — — 4 3 4 3 4 5 3 4 5 3 3 3 4 2 3 3 5 3 4 4 5 All elements have 1 PPT in their linker 4 4 4 4 4 5 3 4 5 3 4 4 4 5 3 3 5 3 4 4 5 4/element Element Lotus2 Osr10 Osr9 Sorghum Medicago Citrus Hopie ToRTL1 SIRE1-1 Endovir1-1 Vitis Barbara Maximus Inga Usier ATCOPIA43 Osr7 Osr8 Tnd-1†† OPIE-2 PREM-2 Avg of Sireviruses Avg of classic copia 12.12/1.68/1.22 11.97/2.04/1.56 11.63/1.68/1.51 12.10/1.79/1.22 11.93/1.14/1.27 9.98/1.28/1.16 11.87/1.37/1.68 9.68/0.88/0.80 9.29/0.52/1.00 9.08/1.55/0.54 9.67/1.10/1.24 9.90/2.76/1.66 14.42/3.96/1.41 12.02/1.61/1.43 11.77/1.84/1.57 9.07/1.59/0.56 8.92/1.31/1.62 9.21/1.10/1.21 8.45/0.73/1.59 8.98/0.79/1.29 9.43/0.82/1.30 10.55/1.50/1.28 5.60/0.078/0.56