The Chromosome-Scale Genome of the Raccoon Dog: Insights into the Genomic Basis of Invasiveness

The raccoon dog (Nyctereutes procyonoides) is a canid native to East Asia, but it has spread widely over Europe since it was introduced for the fur trade in the last century, and it has subsequently become an invasive species listed on the European Union's list of Invasive Alien Species of Concern. Here, we report a chromosome-scale genome of the raccoon dog with high contiguity, completeness, and accuracy, assembled by PacBio and Hi-C technologies. The length of the genome is 2.38 Gb with the scaffold N50 of 83.7 Mb. The identification of a 127.44 Mb X chromosome and a 3.24 Mb Y-linked scaffold were further validated by resequencing 38 individuals. To reveal the possible genomic basis of biological characteristics facilitating its invasiveness, we focused on omnivory, reproduction and immunity. The intact taste receptor genes, expansion of gene families and positively selected genes related to digestion, absorption, foraging, and detoxification likely support its omnivory. Its high reproductivity may be due to several positively selected genes and raccoon dog-specific mutations in TDRD6 and ZP3. A large amount of enriched GO terms on energy metabolism and several KEGG pathways and positively selected innate and adaptive immunity genes were speculated to be closely related to its strong immune system. Finally, we found a long-term population decline with a high level of genetic diversity in the raccoon dog population. This chromosome-scale genome of the raccoon dog provides a valuable resource and insights for understanding its invasive characteristics, as well as ecology and evolution.