This file collection consists of the improved genomic sequences, gene annotations, and evidence tracks that were used by the analyses described in the manuscript “Retrotransposons are the major contributors to the expansion of the Drosophila ananassae Muller F element.” This study seeks to identify the factors that have contributed to the expansion of the D. ananassae F element (> 18.6Mb) compared to the D. melanogaster F element (~5.2 Mb). As part of this study, we performed manual sequence improvement and gene annotations of the D. ananassae F element and the base of the D element. The collection includes the D. ananassae gene annotations and additional notes in the Generic Feature Format Version 3 (GFF3) format. The collection also includes the MySQL database dump and the data files used to create the D. ananassae (Oct. 2015/DanaImproved) assembly on the GEP UCSC Genome Browser (available at http://gander.wustl.edu).