A reference genome was generated using PacBio CLR and Omni-C data.
Genome assembly and raw sequencing data can be found in NCBI BioProject PRJNA1097536. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBCDWE000000000.
The Jonah crab used for the reference genome was a male (carapace width = 175mm) harvested from the Gulf of Maine in May 2021 and purchased from the Fresh Lobster Company (Gloucester, MA). Several tissues (gonad, walking leg muscle, haemocytes, gill, and hepatopancreas) were dissected from the individual and placed in individual 2mL cryovials before being flash-frozen in liquid nitrogen and stored at -80°C until shipment. Frozen gonad and muscle tissue was shipped on dry ice to Dovetail Genomics for library prep and sequencing.
DNA extraction, library prep, and sequencing were performed by Dovetail Genomics, funded by a Revive & Restore Wild Genomes grant. Three PacBio CLR libraries were generated with DNA from gonad tissue. Libraries were CLR, rather than HiFi, due to difficulties generating additional HiFi libraries. Dovetail Genomics also generated Omni-C data for scaffolding using muscle tissue.
Both Dovetail Genomics and GMGI (led by J. Polinski) used the above described sequencing data to generate reference assemblies. The final chromosome-level assembly was generated by GMGI. Information on how that assembly was generated and downstream analyses can be found in the subdirectories of this repository.