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Background  Metazoan digestive systems develop from derivatives of ectoderm, endoderm and mesoderm, and vary in the relative contribution of each germ layer across taxa and between gut regions. In a small number of well-studied model systems, gene regulatory networks specify endoderm and mesoderm of the gut within a bipotential germ layer precursor, the endomesoderm. Few studies have examined expression of endomesoderm genes outside of those models, and thus, it is unknown whether molecular specification of gut formation is broadly conserved. In this study, we utilize a sequenced genome and comprehensive fate map to correlate the expression patterns of six transcription factors with embryonic germ layers and gut subregions during early development in  Capitella teleta .    Results  The genome of  C. teleta  contains the five core genes of the sea urchin endomesoderm specification network. Here, we extend a previous study and characterize expression patterns of three network orthologs and three additional genes by  in situ  hybridization during cleavage and gastrulation stages and during formation of distinct gut subregions. In cleavage stage embryos,  Ct-otx, Ct-blimp1, Ct-bra  and  Ct-nkx2.1a  are expressed in all four macromeres, the endoderm precursors.  Ct-otx, Ct-blimp1,  and  Ct-nkx2.1a  are also expressed in presumptive endoderm of gastrulae and later during midgut development. Additional gut-specific expression patterns include  Ct-otx, Ct-bra ,  Ct-foxAB  and  Ct-gsc  in oral ectoderm;  Ct-otx, Ct-blimp1, Ct-bra  and  Ct-nkx2.1a  in the foregut; and both  Ct-  bra and  Ct-nkx2.1a  in the hindgut.    Conclusions  Identification of core sea urchin endomesoderm genes in  C. teleta  indicates they are present in all three bilaterian superclades. Expression of  Ct-otx, Ct-blimp1  and  Ct-bra , combined with previously published  Ct-foxA  and  Ct-gataB1  patterns, provide the most comprehensive comparison of these five orthologs from a single species within Spiralia. Each ortholog is likely involved in endoderm specification and midgut development, and several may be essential for establishment of the oral ectoderm, foregut and hindgut, including specification of ectodermal and mesodermal contributions. When the five core genes are compared across the Metazoa, their conserved expression patterns suggest that ‘gut gene’ networks evolved to specify distinct digestive system subregions, regardless of species-specific differences in gut architecture or germ layer contributions within each subregion.    Electronic supplementary material  The online version of this article (doi:10.1186/2041-9139-5-39) contains supplementary material, which is available to authorized users.

Molecular conservation of metazoan gut formation: evidence from expression of endomesoderm genes in Capitella teleta (Annelida)