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

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.