Evolution of insect hindwing morphology: A comparative genomic analysis of targets of Hox protein Ultrabithorax. Apis mellifera

To gain insights into the species-specific events downstream of Ubx, we identified direct targets of Ubx from Apis by ChIP-seq and compared them with those of Drosophila at the level of both their function and regulation. While the majority of the targets are species-specific, the ontological distribution of all targets was similar amongst the two species. Interestingly, although considerable number of wing-patterning genes are retained as targets of Ubx over the past 300 millions years, many of them are differentially expressed only between wing and haltere in Drosophila and not between forewing and hindwing in Apis . Detailed bioinfomatics analysis and and experimental validation of enhancer sequences suggest that acquisition of binding sites for additional transcription factors without altering binding per se of Ubx could also contribute to the diversity in Ubx function. Overall design: We carried out ChIP seq on fore and hind wing buds of Apis mellifera (two replicates each) using polyclonal anti Ubx antibody and pre immune IgG from the same animal. We identifed peaks in the chipped samples using input DNA as a reference. All the experiments were carried out on two independent biological replicates.