Whole-genome sequencing data provide a landscape picture of genetic variability in sea cucumber species.

Holothuria is a genus of marine invertebrates commonly called sea cucumbers, that belongs to the phylum Echinodermata. Holothuria species are deposit feeders, ingesting sediment with oral tentacles, extracting and digesting the organic matter with associated microorganisms, and voiding the sand through the anus. In this way they bioturbate significant areas of the seabed, playing a central role in the benthic habitats where these species live. The interest in Holothuria spp. for aquaculture began in Asia and soon reached the European market, making these species promising candidates to establish novel aquaculture production systems worldwide. The genus counts more than 160 species, many of which are uncharacterised at the genome level. Here, we provide a comparative genome analysis between 2 Mediterranean sea cucumber species, Holoturia polii (HP) and Holoturia tubulosa (HT) utilizing the reference genomes of both Holothuria glaberrima (HG) and Holothuria scabra (HS), the only 2 species of this genus for which a reference genome is available thus far. The HG and HS reference genomes are composed of 89,105 and 4,345 scaffolds, respectively. Whole-genome sequencing data sets of 4 HP and 3 HT were produced, filtered and then mapped to the 2 reference genomes with standard options using BWA tool. The genome coverage of the sequencing data obtained for HT was 59.58% and 20.24% against the HG and HS genomes respectively, whereas the genome coverage obtained for HP was 55.62% and 19.16% against the same 2 genomes respectively. Variant calling was performed utilizing the HG-based alignment, retrieved more than 25 million high-quality SNPs. These SNPs were used for the study of population differentiation via the FST statistics; HP and HT that was 0.34 presented a FST index equal to 0.34. This information provided a first comparative analysis of genome information between HT and HP species and underlined the need to further expand genomic research in holothurian species. This information will be used to detect genomic regions of high genetic divergence that might differentiate HT and HP species.