Comparative genomics of the Hondo red fox

We conducted whole-genome shotgun sequencing and reference-guided assembly of the wild Hondo red fox (Vulpes vulpes japonica) for four individuals on the Japanese Archipelago to reconstruct their evolutionary history at a fine scale: two individuals from the Honshu Island and each one individual from the Shikoku and Kyushu islands. We assigned GCF_003160815 (82423 scaffolds from the red fox) to GCA_024500485 (a chromosome-level assembly from the Tibetan sand fox) to prepare the reference genome at a pseudomolecule-level and mapped pair-end reads of each sample to that. See paper for more information.