Figure 5.

Segmental multiplication within a TE cluster in the fly genome. Re-annotation of a cluster of repeats in the Drosophila melanogaster chromosome arm 3R. The scale shows chromosomal coordinates (Release 3.1 genome sequence). Visualisation scheme as in Figure 3, except that "element" models – displayed as boxes united by horizontal lines – no longer indicate sequences sharing an insertion (transposition) event; here a model indicates sequences that resulted from segmental multiplication subsequent to an original insertion. Note the high periodicity of the arrangement. The LTR-elements displayed immediately above the bottom tier all belong to the COPIA2 family, the sequences marked with a '*' are all INVADER1 LTRs, and the ones marked with a black bar are MICROPIA elements. REANNOTATE infers that the COPIA2 sequences have been involved in DNA rearrangements other than transposition of an entire element. It is likely that the INVADER1 LTR was inserted in a COPIA2 LTR prior to the multiplication of the latter. The green box to the left indicates (subsequent) insertion of a PROTOP_A element, and the ones on the right S-elements. (All family names given as in the RU database). This figure was rendered in APOLLO from a GFF annotation file generated by REANNOTATE, and it may be compared with Figure 2 in ref. [32].