Corallimorpharian genome supports the monophyly of Scleractinia and illuminates the cellular evolution of coral calcification
- 1Academia Sinica
Abstract
The production of calcified skeletons by stony corals is the cornerstone of reef ecosystems and the persistence of marine biodiversity. Corallimorpharians, sometimes described as naked corals, resemble stony corals in many respects but lack hardened skeletons. However, whether they are stony corals that secondarily lost their skeletons has been a subject of much debate. Here, we present a chromosome-level genome of the corallimorpharian Ricordea yuma and show that macrosynteny and microsynteny analyses provide strong support for corallimorpharians as the sister group to stony corals. This phylogenetic placement indicates that corallimorpharians were not ancestrally skeletonized and therefore occupy a critical outgroup position for reconstructing the origin of coral calcification. Guided by this phylogenetic context, we sequenced whole-polyp single-cell transcriptomes from R. yuma and the complex coral Galaxea fascicularis and found that the scleractinian skeleton evolved through the emergence of a derived calicoblast cell state in stony corals. A combination of comparative genomics and regeneration experiments in G. fascicularis show that the emergence of the calicoblast cell state was accompanied by the evolution of a biomineralization toolkit assembled from lineage-specific innovations and co-opted ancestral components. Although corallimorpharians retain some ancestral genes later incorporated into coral biomineralization, they lack a detectable calicoblast-like transcriptional state and many core calcification genes. Together, our findings indicate that coral calcification arose through coordinated changes in genome architecture, gene repertoire, and cell identity, highlighting this process as a major evolutionary transition driven by the integration of genomic and cellular innovations.
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BibTeX
@misc{lewin2026corallimorpharian,
title = {{Corallimorpharian genome supports the monophyly of Scleractinia and illuminates the cellular evolution of coral calcification}},
author = {T. D. Lewin and T. Sakagami and V. M. Pinon-Gonzalez and Y. Yoshioka and L.-J. Kao and Y.-L. Chiu and K. Sasaki and Y.-H. Chen and J.-Y. Li and K.-X. Tin and M.-Y. J. Lu and D. J. Miller and S. Shikina and M.-F. Lin and Y.-J. Luo},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.25.754439},
url = {https://www.biorxiv.org/content/10.64898/2026.09.25.754439v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Corallimorpharian genome supports the monophyly of Scleractinia and illuminates the cellular evolution of coral calcification
AU - T. D. Lewin
AU - T. Sakagami
AU - V. M. Pinon-Gonzalez
AU - Y. Yoshioka
AU - L.-J. Kao
AU - Y.-L. Chiu
AU - K. Sasaki
AU - Y.-H. Chen
AU - J.-Y. Li
AU - K.-X. Tin
AU - M.-Y. J. Lu
AU - D. J. Miller
AU - S. Shikina
AU - M.-F. Lin
AU - Y.-J. Luo
PY - 2026
DA - 2026/09/25
PB - bioRxiv
DO - 10.64898/2026.09.25.754439
UR - https://www.biorxiv.org/content/10.64898/2026.09.25.754439v1
AB - The production of calcified skeletons by stony corals is the cornerstone of reef ecosystems and the persistence of marine biodiversity. Corallimorpharians, sometimes described as naked corals, resemble stony corals in many respects but lack hardened skeletons. However, whether they are stony corals that secondarily lost their skeletons has been a subject of much debate. Here, we present a chromosome-level genome of the corallimorpharian Ricordea yuma and show that macrosynteny and microsynteny analyses provide strong support for corallimorpharians as the sister group to stony corals. This phylogenetic placement indicates that corallimorpharians were not ancestrally skeletonized and therefore occupy a critical outgroup position for reconstructing the origin of coral calcification. Guided by this phylogenetic context, we sequenced whole-polyp single-cell transcriptomes from R. yuma and the complex coral Galaxea fascicularis and found that the scleractinian skeleton evolved through the emergence of a derived calicoblast cell state in stony corals. A combination of comparative genomics and regeneration experiments in G. fascicularis show that the emergence of the calicoblast cell state was accompanied by the evolution of a biomineralization toolkit assembled from lineage-specific innovations and co-opted ancestral components. Although corallimorpharians retain some ancestral genes later incorporated into coral biomineralization, they lack a detectable calicoblast-like transcriptional state and many core calcification genes. Together, our findings indicate that coral calcification arose through coordinated changes in genome architecture, gene repertoire, and cell identity, highlighting this process as a major evolutionary transition driven by the integration of genomic and cellular innovations.
ER -