Brachiopod genome unveils the evolution of BMP signalling in bilaterian body patterning

Abstract The molecular control and ancestral state of dorsal–ventral patterning within spiralians remain unclear due to the remarkable diversity across species. Here we present a chromosome-level genome for the brachiopod Lingula anatina and apply functional transcriptomics to study dorsal–ventral patterning under BMP signalling control. We uncover asymmetrical activation of BMP signalling at the dorsal side of the gastrula, governed by ventral chordin expression and a ‘seesaw’ of BMP ligands. Using small-molecule drugs and recombinant proteins, we show that high BMP activity inhibits genes typically associated with neural patterning during gastrula and larval stages, similar to deuterostomes and non-spiralian protostomes. Our findings suggest deep conservation of this mechanism across all three major bilaterian clades, supported by striking similarities in BMP-regulated gene sets between brachiopods and Xenopus. We argue that the spiralian ancestor retained the ancestral bilaterian mechanism, although downstream network components have undergone developmental system drift.