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Background  Unlike  Drosophila  but similar to other arthropod and vertebrate embryos, the flour beetle  Tribolium castaneum  develops everted limb buds during embryogenesis. However, the molecular processes directing the evagination of epithelia are only poorly understood.    Results  Here we show that the newly discovered genes  Tc-flipflop1  and  Tc-flipflop2  are involved in regulating the directional budding of appendages. RNAi-knockdown of  Tc-flipflop  results in a variety of phenotypic traits. Most prominently, embryonic limb buds frequently grow inwards rather than out, leading to the development of inverted appendages inside the larval body. Moreover, affected embryos display dorsal closure defects. The  Tc-flipflop  genes are evolutionarily non-conserved, and their molecular function is not evident. We further found that  Tc-RhoGEF2 , a highly-conserved gene known to be involved in actomyosin-dependent cell movement and cell shape changes, shows a  Tc-flipflop -like RNAi-phenotype.    Conclusions  The similarity of the inverted appendage phenotype in both the  flipflop - and the  RhoGEF2  RNAi gene knockdown led us to conclude that the  Tc-flipflop  orphan genes act in a Rho-dependent pathway that is essential for the early morphogenesis of polarised epithelial movements. Our work describes one of the few examples of an orphan gene playing a crucial role in an important developmental process.    Electronic supplementary material  The online version of this article (10.1186/s12983-017-0234-9) contains supplementary material, which is available to authorized users.

The flipflop orphan genes are required for limb bud eversion in the Tribolium embryo