  Here, we provide revised gene models for D. ananassae, D. yakuba, and D.
simulans, which include UTRs and empirically verified intron-exon boundaries,
as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast
comparison. Using these revised annotations, we perform differential expression
testing using the cufflinks suite to provide a broad overview of differential
expression between reproductive tissues and the carcass. We identify thousands
of genes that are differentially expressed across tissues in D. yakuba and D.
simulans, with roughly 60% agreement in expression patterns of orthologs in D.
yakuba and D. simulans. We identify several cases of putative polycistronic
transcripts, pointing to a combination of transcriptional read-through in the
genome as well as putative gene fusion and fission events across taxa. We
furthermore identify hundreds of lineage specific genes in each species with no
blast hits among transcripts of any other Drosophila species, which are
candidates for neofunctionalized proteins and a potential source of genetic
novelty.
