Red Fox Chromosomal Fragment Assembly. Vulpes vulpes breed:Hybrid Novosibirsk

The development of genomic tools for the red fox requires that the genome be assembled at the chromosome scale. The scaffolds from the draft red fox assembly (BioProject PRJNA378561) were aligned against the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify conserved sequences among the three species. The program Reference-Assisted Chromosome Assembly (RACA) integrated this syntenic information with the mapping of the sequencing reads against the scaffolds to assemble 128 fragments. Markers with known positions on the fox meiotic linkage map were then mapped onto the RACA fragments and used to guide the assembly of these fragments into 40 large fragments on the scale of fox chromosome arms. The new assembly contains 93% of the draft genomic sequence by length.