Extended Data Figure 9: Identification of putative Shellder copies in D. simulans and D. mauritiana populations.
From: Natural courtship song variation caused by an intronic retroelement in an ion channel gene
a, Schematic of the Shellder insertion at the slo locus in sim5. Shellder contains three open reading frames (ORFs) resembling the gag, pol, and env genes of a retrovirus, flanked by 458 bp long terminal repeats (LTRs). Putative core protein domains are indicated: PR, protease; RT, reverse transcriptase; RH, RNase H; INT, integrase. In other retroviruses, the pol ORF often includes a 5′ protease ___domain. Shellder contains a conserved protease ___domain 5′ of the predicted pol start codon. It is possible that the Shellder pol ORF uses a non-ATG start codon. TSR, target site repeat. P1, P2, and P3 represent the three LTR-specific primers used for TagMap. b, Putative Shellder copies in D. simulans (blue) and D. mauritiana (orange) wild-type strains identified by TagMap. The slo locus insertion in sim5 is indicated and is unique amongst these samples. Shellder insertions are enriched near centromeres (grey ovals), but can also be found in the euchromatic regions. Precise mapping locations are provided in Supplementary Table 5. This is probably an incomplete survey of Shellder copies, because TagMap may be biased towards detecting young and intact copies of transposable elements.
