The Foldback -like element Galileo belongs to the P superfamily of DNA transposons and is widespread within the Drosophila genus

Marzo et al. 10.1073/pnas.0712110105.

Supporting Information

Files in this Data Supplement:

SI Table 1
SI Table 2
SI Table 3
SI Table 4
SI Table 5
SI Table 6
SI Figure 5
SI Table 7
SI Figure 6
SI Table 8
SI Figure 7
SI Table 9

SI Figure 5

Fig. 5. Neighbor-joining phylogenetic tree built with 14 Galileo copies found in the D. virilis genome by using MEGA (16409 is the most-complete copy, see Fig. 1B). The two TIRs of each copy were included in the tree as separate sequences to allow their comparison within and between copies. TIRa is the TIR located at 5' from the TPase or the first TIR that appears in the contig if the copy could not be oriented. The complete deletion option was used leaving 76 informative sites (an almost identical tree results when omitting some of the shortest sequences, increasing the number of informative sites to 258). Bootstrap values of main nodes are shown. Groups A and B show a ~68% divergence indicating ~20 myr of separation. Details of these Galileo copies are given in SI Tables 4 and 5.

SI Figure 6

Fig. 6. Multiple alignment of 22 proteins: eight Galileo TPases, eigth 1360 TPases, five representative P element TPases and THAP9 protein from Homo sapiens. The alignment of the THAP domain region was corrected by hand to align the functional and conserved amino acids of the domain. Conserved blocks selected with Gblocks are marked with a blue box. Identical positions are black-shaded and the positions with similar amino acids are gray-shaded. THAP domain conserved residues are marked with a red star and the three final residues (AVP) are included in a red box. A red line marks the entire THAP domain region. The coiled-coil region is marked with an orange-filled box. The Leucine amino acids of the Leucine zipper coiled-coil motif of the Dmel\P TPase are marked with a yellow triangle. GTP binding sites of the Dmel\P TPase are marked with a yellow-filled box. The catalytic amino acids are labeled with a green star. The fourth acidic catalytic amino acid of the P element transposase that is not conserved in the TPases of Galileo and 1360 is indicated with a gray star. Accession numbers for P element TPases and THAP9 are: Dmel\P: Q7M3K2, Dbif\P: AAB31526, Dhel\P: AAK08181, Dwil\P: AAT96022, Spal\P: M63341, THAP9: NP_078948.

SI Figure 7

Fig. 7. Isolation of Galileo in D. buzzatii. (A) Molecular structure of the putative full Galileo element from D. buzzatii. The big blue arrows are the TIRs and the white rectangle is the ORF coding for the TPase with the THAP domain shown in red. Primer location is indicated by small arrows underneath. (B) PCR amplification of the full Dbuz\Galileo copy. Four PCR reactions yielded relatively long products that were subsequently sequenced and assembled. The fact that each PCR product produced a single nucleotide sequence and that the overlapping portions between the four sequences were 99.99% identical (a single mismatch), suggests that they come from a single genomic Galileo copy. The sequence of the TIR ends was taken from the previously known D. buzzatii Galileo-3 sequence (accession no. AF368897). (C) Sequences of the primers used for amplification and sequencing of PCR products. Primers M13F and M13R are universal primers from the sequencing vector, bacteriophage M13.