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

Abstract

Genomic data for the closest relatives of house mice (Mus musculus 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, Mus spicilegus Using read cloud sequencing and de novo 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 Mus species. To evaluate the utility of the M. spicilegus genome for behavioral and ecological genomics, we extracted 196 vomeronasal receptor (VR) sequences from our genome and analyzed phylogenetic relationships between M. spicilegus VRs and orthologs from M. musculus and the Algerian mouse, M. spretus While most M. spicilegus VRs clustered with orthologs in M. musculus and M. spretus, 10 VRs with evidence of rapid divergence in M. spicilegus are strong candidate modulators of species-specific chemical communication. A high quality assembly and genome for M. spicilegus 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 M. spicilegus unique.

Keywords: Mus spicilegus; de novo genome assembly; mound-building mouse; read cloud; vomeronasal receptors.

Figure 1

The geographic distribution of the mound-building mouse, Mus spicilegus. Inset: Mound-building mice are highly social and exhibit natural burrowing behavior under laboratory conditions. Au, Austria; Hu, Hungary; Se, Serbia; Bu, Bulgaria; M, Moldova; A, Albania; G, Greece. Distribution based on Coroiu et al. (2016). Photo, AG Ophir.

Figure 2

Phylogenetic relationships among the two major vomeronasal receptor subfamilies, V1Rs (A) and V2Rs (B) in M. spicilegus (MUSP, red branches and gene names), M. musculus (MUMU, black branches and gene names), and M. spretus (SPRET, green branches and gene names). Trees are unrooted cladograms, open circles on nodes indicate bootstrap support >90. Red arrowheads indicate M. spicilegus receptors that are not sister to orthologs with the same name in either M. musculus or M. spretus. Gene names with an underscore and number appended are transcript variants in M. musculus. Gene names with “like” appended are unannotated putative VRs in the M. spretus genome. M. spicilegus VR sequences are provided in Supplemental Material (V1Rs: File S1; V2Rs: File S2).