Eupentacta fraudatrix: the first chromosome-level holothurian genome with extraordinarily high heterozygosity

Eupentacta fraudatrix is the only species of sea cucumbers for which transdifferentiation has been described. This type of cell type switching occurs during gut regeneration after evisceration, which makes this species a scientifically valuable model for studying regeneration mechanisms. Moreover, chromosome-level genomes for the family Sclerodactylidae have not been available until now. In this study, we employed the MGI short-read, Oxford Nanopore, and Hi-C technologies to assemble and annotate two chromosome-level, high-quality haplotypes of E. fraudatrix. The estimated heterozygosity was 5.1%, which is much higher than the known values for sea cucumber genomes. Both haplotypes are nearly equivalent, containing 23 chromosomes with a total length of approximately 1.6 gigabase pairs, and 99% of assembled bases anchored to chromosome-level scaffolds. The annotation predicted 26,352 protein-coding genes for one haplotype and 25,238 genes for the other, with BUSCO assessment revealing 98.1 and 97.9% complete metazoa_odb12 core genes. The chromosome-level assembly and annotation of E. fraudatrix genome will provide a genomic basis for further phylogenetic, comparative, and molecular biological studies of echinoderm regeneration.