Y-Chromosome Markers for the Red Fox

Abstract

The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated the development of genomic tools for the species. Efforts to identify the population history of red foxes in North America have previously been limited by a lack of information about the red fox Y-chromosome sequence. However, a megabase of red fox Y-chromosome sequence was recently identified over 2 scaffolds in the reference genome. Here, these scaffolds were scanned for repeated motifs, revealing 194 likely microsatellites. Twenty-three of these loci were selected for primer development and, after testing, produced a panel of 11 novel markers that were analyzed alongside 2 markers previously developed for the red fox from dog Y-chromosome sequence. The markers were genotyped in 76 male red foxes from 4 populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland (eastern United States), and 9 from the island of Great Britain, as well as 48 foxes of known North American origin maintained on an experimental farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes among these red foxes, whereas the 2 previously known markers alone would have identified only 10 haplotypes. The haplotypes from the 4 populations clustered primarily by continent, but unidirectional gene flow from Great Britain and farm populations may influence haplotype diversity in the Maryland population. The development of new markers has increased the resolution at which red fox Y-chromosome diversity can be analyzed and provides insight into the contribution of males to red fox population diversity and patterns of phylogeography.

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly

“…The chromosomal fragments contain 93.7% of the 2.5 Gbp of sequence originally reported [ 12 ]. Additionally, a minimum of 0.05% of the sequence contained in the original genome is derived from the Y-chromosome [ 14 ]. Thus, although the refined fox assembly incorporates genomic information from only 398 large scaffolds of the 676,878 scaffolds assembled, this corresponds to a loss of less than 3.5% of sequence information from the draft genome.…”

“…The scaffolds included in the assembly spanned approximately the full range of sizes (50 to 55,683 Kbp) whereas the excluded scaffolds tended to be smaller (48 to 656 Kbp). The outlier points shaded in blue represent scaffolds 292 and 310, which were experimentally demonstrated to contain red fox Y-chromosome sequence [ 14 ], and therefore would not be expected to be included in RACA’s assembled fragments.…”

“…Adaptation and response to selection in the red fox is therefore of interest not only to wildlife ecology, but also fields including behavioral and evolutionary genetics. The draft red fox genome assembly, which is currently in version 2.2 and known as vv2.2, has already proven valuable for studies of fox behavioral genetics [ 12 ], immunological adaptation [ 13 ], and population diversity [ 14 ].…”

Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions

“…Finally, reads of 30 nucleotides or longer were selected and mapped to the reference genome. In the absence of a complete fox genome assembly, [36][37][38] closely related dog genome assembly (C. familiaris 3.1 genome) was used as the reference for mapping. This reference genome was also used in previous studies comparing the PFC, BFB and pituitary gland of tame vs aggressive foxes.…”

The Red Fox Y-Chromosome in Comparative Context

“…The draft genome is organized in 676,878 scaffolds ranging in size from as large as 55.7 Mb to as small as 100 bp, with a scaffold N50 of 11.8 Mbp [27]. Preliminary analysis [28] of two scaffolds found to show higher synteny with the dog Y-chromosome than any other dog chromosome facilitated the development of 11 novel male-specific microsatellite markers that were used to conduct a preliminary analysis of patterns of diversity across red fox populations. Although the development of genomic resources for the red fox has focused primarily on experimentally bred tame and aggressive lines developed and maintained through the Russian Farm Fox Experiment at the Institute for Cytology and Genetics in Novosibirsk, Russia [29], the preliminary analysis of inter-population diversity using the 13 microsatellite markers suggested that resources developed in farm-bred foxes are still useful for ascertaining variation in geographically diverse populations [28].…”