R7-dependent transcription in the developing Drosophila retina

Color vision in Drosophila is mediated by photoreceptors R7 and R8, which express various combinations of opsins Rh3, Rh4, Rh5 and Rh6 depending on their cellular identity. Most ommatidia are classified as either “pale” or “yellow” subtypes with pale ommatidia coordinately expressing Rh3 and Rh5—in R7 and R8 cells respectively—while yellow express Rh4 and Rh6. Subtype identity is established initially in R7 photoreceptors via a stochastic mechanism then transmitted to the R8 via an inductive signal to ensure paired opsin expression. To identify factors that may be involved in this process, we used RNA-Seq to detect genes that are differentially expressed in sevenless mutant retinas at 40 hours after puparium formation. Since loss of sevenless prevents R7 recruitment and specification, we reasoned that this approach would allow us to identify genes that are enriched in R7 cells during this critical time point. Furthermore, since it has previously been established that in the absence of R7 most R8s will adopt the yellow Rh6-expressing identity, this gives us the opportunity to identify genes which may inductive mechanism occurring in R8 cells. Overall design: Replicate samples (four per genotype) were prepared from dissected 40 hour apf female pupal retinas from w[1118] control or w[*] sev[14] animals. Normalized count data from RNA-Seq was used to identify differentially espressed transcripts.