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In the fruitfly  Drosophila melanogaster , the differential development of wing and haltere is dependent on the function of the Hox protein Ultrabithorax (Ubx). Here we compare Ubx-mediated regulation of wing patterning genes between the honeybee,  Apis mellifera , the silkmoth,  Bombyx mori  and  Drosophila . Orthologues of Ubx are expressed in the third thoracic segment of  Apis  and  Bombyx , although they make functional hindwings. When over-expressed in transgenic  Drosophila , Ubx derived from  Apis  or  Bombyx  could suppress wing development, suggesting evolutionary changes at the level of co-factors and/or targets of Ubx. To gain further insights into such events, we identified direct targets of Ubx from  Apis  and  Bombyx  by ChIP-seq and compared them with those of  Drosophila . While majority of the putative targets of Ubx are species-specific, a considerable number of wing-patterning genes are retained, over the past 300 millions years, as targets in all the three species. Interestingly, many of these are differentially expressed only between wing and haltere in  Drosophila  but not between forewing and hindwing in  Apis  or  Bombyx . Detailed bioinformatics and experimental validation of enhancer sequences suggest that, perhaps along with other factors, changes in the cis-regulatory sequences of earlier targets contribute to diversity in Ubx function.

A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species