The Red Fox Y-Chromosome in Comparative Context

• Published in: Genes Vol. 10; no. 6; p. 409
• Main Authors: Rando, Halie M, Wadlington, William H, Johnson, Jennifer L, Stutchman, Jeremy T, Trut, Lyudmila N, Farré, Marta, Kukekova, Anna V
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 28.05.2019; MDPI
• Subjects: Animal behavior; Animals; Artificial chromosomes; BCORY2; Canis lupus familiaris; Canis lupus lupus; Carnivora - genetics; carnivore; Cats; Copy number; copy-number variation; DNA Copy Number Variations - genetics; Dogs; Felis catus; Female; Females; Foxes; Foxes - genetics; Genes; Genome; Genomes; Male; Males; Mammals; Mitochondrial DNA; MSY; Next-generation sequencing; Nucleotide sequence; Phylogeny; Proteins; sex chromosomes; Species; UBE1Y; Vulpes vulpes; Wolves - genetics; X chromosomes; Y Chromosome - genetics; Y chromosomes; Y-chromosome; Y-chromosome genes; MSY; next-generation sequencing; copy-number variation; BCORY2; carnivore; Y-chromosome; UBE1Y; sex chromosomes; Vulpes vulpes; Y-chromosome genes
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes10060409

While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat ( ), dog ( ), and grey wolf ( ), providing the opportunity to examine the red fox ( ) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific -mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of and than has been reported in related species and fewer copies of than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.