A High Quality Genome for <i>Mus spicilegus</i>, a Close Relative of House Mice with Unique Social and Ecological Adaptations

Abstract

Genomic data for the closest relatives of house mice (<i>Mus musculus</i> species complex) are surprisingly limited. Here, we present the first complete genome for a behaviorally and ecologically unique member of the sister clade to house mice, the mound-building mouse, <i>Mus spicilegus</i> Using read cloud sequencing and <i>de novo</i> assembly we produced a 2.50 Gbp genome with a scaffold N50 of 2.27 Mbp. We constructed >25 000 gene models, of which the majority had high homology to other <i>Mus</i> species. To evaluate the utility of the <i>M. spicilegus</i> genome for behavioral and ecological genomics, we extracted 196 vomeronasal receptor (VR) sequences from our genome and analyzed phylogenetic relationships between <i>M. spicilegus</i> VRs and orthologs from <i>M. musculus</i> and the Algerian mouse, <i>M. spretus</i> While most <i>M. spicilegus</i> VRs clustered with orthologs in <i>M. musculus</i> and <i>M. spretus</i>, 10 VRs with evidence of rapid divergence in <i>M. spicilegus</i> are strong candidate modulators of species-specific chemical communication. A high quality assembly and genome for <i>M. spicilegus</i> will help to resolve discordant ancestry patterns in house mouse genomes, and will provide an essential foundation for genetic dissection of phenotypes that distinguish commensal from non-commensal species, and the social and ecological characteristics that make <i>M. spicilegus</i> unique.