This project collects the genomic data generated for Phakellia ventilabrum, the chalice sponge, to facilitate genome assembly. The data was produced in collaboration with the ERGA sample ambassador Ana Riesgo (Spain), and the ERGA Pilot Project team. The European Reference Genome Atlas (https://www.erga-biodiversity.eu/) is an affiliated project under the umbrella of the Earth BioGenome Project. Please see the ERGA Pilot Project Data Sharing and Management Policy (https://doi.org/10.5281/ZENODO.8091290) prior to publication using this data.