Yoshioka, Yuki, Yamashita, Hiroshi, Uchida, Taiga, Shinzato, Chuya, Kawamitsu, Mayumi, Fourreau, Chloé Julie Loïs, Castelló, Guillermo Mironenko, Fiedler, Britta Katharina, van den Eeckhout, Timotheus Maximilian, Borghi, Stefano, Reimer, James Davis, and Shoguchi, Eiichi (2024) Azooxanthellate Palythoa (Cnidaria: Anthozoa) Genomes Reveal Toxin-related Gene Clusters and Loss of Neuronal Genes in Hexacorals. Genome Biology and Evolution, 16 (9).

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Abstract

Zoantharia is an order among the Hexacorallia (Anthozoa: Cnidaria), and includes at least 300 species. Previously reported genomes from scleractinian corals and actiniarian sea anemones have illuminated part of the hexacorallian diversification. However, little is known about zoantharian genomes and the early evolution of hexacorals. To explore genome evolution in this group of hexacorals, here, we report de novo genome assemblies of the zoantharians Palythoa mizigama (Pmiz) and Palythoa umbrosa (Pumb), both of which are members of the family Sphenopidae, and uniquely live in comparatively dark coral reef caves without symbiotic Symbiodiniaceae dinoflagellates. Draft genomes generated from ultra-low input PacBio sequencing totaled 373 and 319 Mbp for Pmiz and Pumb, respectively. Protein-coding genes were predicted in each genome, totaling 30,394 in Pmiz and 24,800 in Pumb, with each set having ∼93% BUSCO completeness. Comparative genomic analyses identified 3,036 conserved gene families, which were found in all analyzed hexacoral genomes. Some of the genes related to toxins, chitin degradation, and prostaglandin biosynthesis were expanded in these two Palythoa genomes and many of which aligned tandemly. Extensive gene family loss was not detected in the Palythoa lineage and five of ten putatively lost gene families likely had neuronal function, suggesting biased gene loss in Palythoa. In conclusion, our comparative analyses demonstrate evolutionary conservation of gene families in the Palythoa lineage from the common ancestor of hexacorals. Restricted loss of gene families may imply that lost neuronal functions were effective for environmental adaptation in these two Palythoa species.

Item ID:	85478
Item Type:	Article (Research - C1)
ISSN:	1759-6653
Copyright Information:	© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Date Deposited:	14 May 2025 01:31
FoR Codes:	31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310499 Evolutionary biology not elsewhere classified @ 50% 31 BIOLOGICAL SCIENCES > 3105 Genetics > 310509 Genomics @ 50%
SEO Codes:	28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences @ 100%
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