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

Holothuria or sea cucumber is a genus of marine invertebrates, belonging to the group Echinodermata, commonly called sea cucumbers. Holothuria species are detritivores, raking sand into their mouth with oral tentacles, extracting and digesting the bacteria, animal and vegetal particles, and voiding the sand through the anus. In this way they churn up significant areas of the seabed, playing a central role in the habitat these species live. Holothuria species have been seen as a promising candidate for aquaculture, as they are resistant to handling and adapt easily to captivity conditions. The interest in Holothuria for aquaculture began in Asia and reached the European market, making it a potentially valuable species for European aquaculture. The genus counts more than 160 species, many of which are uncharacterised at the genome level. However, very recently, few genome drafts became available, allowing to conduct genomic analyses on these species. Here, we provide a first comparative genome analysis of two species of sea cucumber that are common along Italian shores, Holoturia polii (HP) and Holoturia tubulosa (HT) utilizing the reference genome of Holothuria glaberrima (HG) in the comparison, the only reference genome so far available. The reference genome is composed of 89,105 scaffolds, most of them (54,676) with scaffolds below 10 kbp in size. Scaffolds over 10 kbp represent 1.067Gb of the predicted 1.1Gb. We produced whole genome sequencing datasets using Illumina paired-end read for a few HP and HT samples. About 300 million reads per sample were filtered and then mapped to the HG reference genome with standard options. Variant calling was performed considering all samples together. The genome coverage from the datasets of HP and HT was 56% and 58%, respectively. This relatively low coverage is probably linked to the drafted genome assembly for HG, which is highly fragmented. Variant calling produced 72,217,418 single nucleotide polymorphisms (SNPs), mostly on the longer scaffolds that will constitute the core of the analyses. This information has been used to estimate the genetic relationship among the three species and detect genomic regions of high genetic divergence that might be useful to define specific genome regions that characterize different Holothuria species. Acknowledgements This study was supported by HOLOTHURIA project funded by Italian Ministry of Agriculture, Food Sovereignty and Forestry (MASAF) grant n. J56J20000150001.