Matsuda, R.; Hosono, C.; Saigo, K.; Samakovlis, C.

Branched tubular organs represent a common solution to the problem of fluid transport in large animals. The growth of new branches has been extensively studied but the regulation of branch pruning remains underexplored. Here, we investigate branch removal in the stereotyped branching patterns of the developing Drosophila airways. After progenitor invagination, the tips of the distal airways generate a stereotyped branching pattern in each central metameric unit. An intriguing exception in the repeating patterns is the lack of branches targeting the visceral mesoderm (visceral primary branch, VB) in the third and nineth metameres. We show that these branches initially form but the localized expression of the pro-apoptotic gene reaper and resultant apoptosis prune them. We reveal that VB3/9 pruning entails four sequential programs. First, a common distal outgrowth program promotes budding and extension of the primary branches, including VB3 and 9. Second, a VB identity program is established representing the ground state of all primary branches. Third, the Bithorax-Complex transcription factors define metameric identities and interfere with the VB program to induce reaper and apoptosis specifically in VB3/9 in a concentration dependent manner. Finally, the default VB cell identity is transformed by extrinsic BMP/Decapentaplegic and WNT/Wingless into more derived primary branch identities and spared from pruning in metamers 3 and 9. Our results demonstrate that molecular and genetic circuits promoting branch emergence and extension can be regionally modified and deployed also for branch pruning.