De novo assembly and annotation of the singing mouse genome

Abstract

BackgroundDeveloping genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits.Specifically, organisms that exhibit unique, accessible phenotypes-of-interests, allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alstons singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. ResultsUsing PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. ConclusionsThese resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.