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.
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Data availability
Genome sequencing and RNA sequencing datasets are accessible through NCBI BioProject under accession number PRJNA1068743. The L. anatina genome is made available on NCBI with the accession GCA_051362555.1 [https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_051362555.1/]. A L. anatina genome browser with a BLAST function is available at https://marinegenomics.oist.jp/lan_3_0/viewer/info?project_id=124. The genome sequence, gene models, and functional annotations from UniProt, Pfam, InterProScan, EggNOG and KOfam are also available at this location. Genomic, transcriptomic and imaging data from this study, including the genome assembly, gene annotations, repeat annotations, gene expression matrices and original Zeiss LSM imaging files, are available on Zenodo (https://doi.org/10.5281/zenodo.16916709). Source data are provided with this paper.
Code availability
Code for analyses in this study is available on GitHub (https://github.com/symgenoevolab/lingula_genome) and Zenodo (https://doi.org/10.5281/zenodo.18591213).
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Acknowledgements
We acknowledge the permission from Amami City, Kagoshima, Japan, for collecting L. anatina specimens. We thank Ryo Koyanagi in the OIST DNA Sequencing Section for his support of RNA sequencing and Asuka Sentoku for support with the embryonic experiment at the University of Ryukyu. We also thank Keisuke Nakashima for a gift of chitin-binding probes and Jr-Kai Yu for support with microscopy. We are grateful to Konstantin Khalturin for facilitating the shipment of fixed embryos from Japan to the USA and to D. Marcela Bolaños for handling the shipment from the USA to Taiwan. This work was supported in part by multiple funding sources over the past decade, including a Japan Society for the Promotion of Science Grant-in-Aid for JSPS Research Fellows (15J01101), a Royal Society Newton International Fellowship (NIF\R1\201315), an Academia Sinica Career Development Award (AS-CDA-112-L06), an Academia Sinica Grand Challenge Program Seed Grant (AS-GCS-114-L08), and National Science and Technology Council Research Project Grants (113-2311-B-001-026 and 114-2311-B-001-024-MY3) to Y.-J.L., T.S. was supported by a JSPS Overseas Research Fellowship. Y.H.W. was supported by the Innovation Team Project of Universities in Guangdong Province (2023KCXTD028) and the National Natural Science Foundation of China General Program (42276104). We thank the Symbiosis Genomics and Evolution Lab members for their assistance and support, and three anonymous reviewers for their insightful comments.
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T.D.L., Y.-J.L. conceived the project. K.S., K.E., N.S. and Y.-J.L. collected specimens. Y.H.W. sequenced the chromosome-scale genome and tissue transcriptomes. T.D.L. and M.-E.C. annotated the genomes. Y.-J.L. conducted embryonic experiments and functional transcriptomics. T.S., K.S., L.-J.K., Y.-L.C. and Y.-J.L. performed whole mount in situ hybridisation. T.D.L., I.J.-Y.L. and Y.-J.L. prepared code for GitHub. K.H. prepared the genome browser. T.D.L. and Y.-J.L. analysed data and wrote the manuscript. K.E., P.W.H.H. and Y.H.W. discussed the results and edited the manuscript. All authors contributed to the revision of the manuscript.
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Lewin, T.D., Sakagami, T., Shimizu, K. et al. Brachiopod genome unveils the evolution of BMP signalling in bilaterian body patterning. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70403-5
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DOI: https://doi.org/10.1038/s41467-026-70403-5
