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

The Eupentacta fraudatrix is the only species of sea cucumbers for which transdifferentiation has been described. That sort of cell type switching occurs during intestinal regeneration after evisceration. Because of this that species is scientifically valuable model for studying regeneration mechanisms. Moreover, chromosome-level genomes for Sclerodactylidae family have not been available until now. In this study, we utilized MGI short-read, Oxford Nanopore and Hi-C technologies to assemble and annotate two chromosome-level, high-quality haplotypes of E. fraudatrix. The esimated heterozygosity was 5%, which is much higher than the known values for sea cucumbers and even slightly higher than that of the Strongylocentrotus purpuratus genome. Both haplotypes are nearly equivalent, containing 23 chromosomes with a total length of approximately 1600 Mbp, and 99% of nucleotides of the raw assembly were anchored to chromosome-level scaffolds. Annotation predicted 26,360 protein-coding genes for one haplotype and 25,232 genes for other, with BUSCO assessment revealing 98.1% and 97.9% complete metazoa_odb12 core genes. This chomosome-level assembly and annotations will provide an genomic basis for further phylogenetic, comparative, and molecular biological studies of echinoderm regeneration.