Gene models for <em>Drosophila ananassae</em>, <em>Drosophila bipectinata</em>, <em>Drosophila kikkawai</em>, and <em>Drosophila takahashii</em>

These files are gene annotations for the genome assemblies described in the forthcoming publication Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae. RefSeq gene models from D. kikkawai, D. takahashii, D. bipectinata, and D. ananassae were aligned against the corresponding Hi-C genome assembly using BLAT with the following parameters q=rna -fine -minScore=20 -stepSize=5. The transcript alignments were analyzed by pslReps with the parameters -minCover=0.15 -minAli=0.98 -nearTop=0.001, and then filtered by pslCDnaFIlter with the parameters -minId=0.95 -minCover=0.15 -localNearBest=0.001 -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap.