A chromosome-level genome assembly for the brown sea cucumber from the Galápagos Islands, Isostichopus fuscus.

The Galápagos Islands face threats from human activities and climate change, with significant consequences for native fauna like the brown sea cucumber, Isotichopus fuscus (Ludwig, 1875). Once abundant in the region's shallow coastal waters, this species has suffered dramatic population declines due to overexploitation and is now listed as endangered by the IUCN and protected under CITES. To support genomics-informed conservation efforts, we employed Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to create a high-quality chromosome-level genome assembly, which was subsequently annotated using RNA-seq-informed gene prediction. The resulting assembly spans 898.4 Mb, with a contig N50 of 21.5 Mb, a scaffold N50 of 36.9 Mb, and a BUSCO completeness score of 98.4%-quality statistics comparable to those of other chromosome-scale assemblies for sea cucumbers in the Stichopodidae family. Consistent with those species, our assembly features 23 chromosomes. The newly available genomic resources for I. fuscus will be important for studies on population genomics, comparative genomics, and the impact of environmental stressors on local adaptation.