The Red Fox Y-Chromosome in Comparative Context.

Area of Science:

• Genomics
• Mammalian Genetics
• Comparative Genomics

Background:

• Mammalian genome assemblies are advancing, but Y-chromosome assemblies lag due to high repeat content and short-read sequencing challenges.
• Existing partial Y-chromosome assemblies for cat, dog, and grey wolf allow for comparative analysis with the red fox.

Purpose of the Study:

• To identify and characterize the Y-chromosome sequence within the red fox (Vulpes vulpes) draft genome.
• To provide a resource for future studies on canid Y-chromosome evolution.

Main Methods:

• A data-driven approach was used to identify Y-chromosome scaffolds from the red fox genome assembly.
• Scaffolds containing known Y-chromosome genes from related species were identified.
• Analysis of male-specific k-mers and inter-sex copy number variation in resequenced fox genomes was performed.

Main Results:

• 171 scaffolds totaling 3.37 Mbp of putative Y-chromosome sequence were identified.
• Gene content is broadly consistent with other carnivore Y-chromosomes.
• The red fox Y-chromosome shows higher copy numbers of BCORY2 and UBE1Y and lower copy numbers of SRY compared to related canids.

Conclusions:

• This study successfully assigned Y-chromosome sequence to the red fox draft genome.
• The findings provide insights into Y-chromosome evolution within canids.
• The identified sequences serve as a valuable resource for further genomic and evolutionary research.