The First De Novo HiFi Genome Assemblies for Three Clownfish-hosting Sea Anemone Species (Anthozoa: Actiniaria)

Abstract The symbiosis between clownfish and giant tropical sea anemones (Order Actiniaria) is one of the most iconic on the planet. Distributed on tropical reefs, 28 species of clownfishes form obligate mutualistic relationships with 10 nominal species of venomous sea anemones. Our understanding of the symbiosis is limited by the fact that most research has been focused on the clownfishes. Chromosome-scale reference genomes are available for all clownfish species, yet only short reads–based reference genomes are available for five species of host sea anemones. Recent studies have shown that the clownfish-hosting sea anemones belong to three distinct clades of sea anemones that have evolved symbiosis with clownfishes independently. Here we present the first high-quality long-read assemblies for three species of clownfish-hosting sea anemones belonging to each of these clades: Entacmaea quadricolor, Stichodactyla haddoni, and Radianthus doreensis. PacBio HiFi sequencing yielded 1,597,562, 3,101,773, and 1,918,148 million reads for E. quadricolor, S. haddoni, and R. doreensis, respectively. All three assemblies were highly contiguous and complete with N50 values above 4 Mb and BUSCO completeness above 95% on the Metazoa dataset. Genome structural annotation with BRAKER3 predicted 20,454, 18,948, and 17,056 protein-coding genes in E. quadricolor, S. haddoni, and R. doreensis genome, respectively. These new resources will form the basis of comparative genomic analyses that will allow us to deepen our understanding of this mutualism from the host perspective.