Spatial transcriptomics reveals a cnidarian segment polarity program in Nematostella vectensis

During early animal evolution, the emergence of axially polarized segments was central to the diversification of complex bilaterian body plans. Nevertheless, precisely how and when segment polarity pathways arose remains obscure. Here, we demonstrate the molecular basis for segment polarization in developing larvae of the sea anemone Nematostella vectensis. Utilizing spatial transcriptomics, we first constructed a 3D gene expression atlas of developing larval segments. Capitalizing on accurate in silico predictions, we identified Lbx and Uncx, conserved homeodomain-containing genes that occupy opposing subsegmental domains under the control of both bone morphogenetic protein (BMP) signaling and the Hox-Gbx cascade. Functionally, Lbx mutagenesis eliminated all molecular evidence of segment polarization at the larval stage and caused an aberrant mirror-symmetric pattern of retractor muscles (RMs) in primary polyps. These results demonstrate the molecular basis for segment polarity in a non-bilaterian animal, suggesting that polarized metameric structures were present in the Cnidaria-Bilateria common ancestor over 600 million years ago. •Nematostella endomesoderm transcriptionally resembles the bilaterian mesoderm•A 3D gene expression atlas helps to characterize segmental identity in Nematostella•Homeobox-containing genes Lbx and Uncx establish segment polarity in Nematostella•The Cnidaria-Bilateria common ancestor likely possessed polarized segments He et al. employ a spatial transcriptomic approach to reveal the presence of a segment polarity program in the cnidarian Nematostella vectensis. Two conserved homeodomain-containing genes, Lbx and Uncx, establish opposing molecular identities within endomesodermal segments and regulate the patterning of segmentally polarized retractor muscles.