Mapping Muroids: Enabling genomic research on an ecological relevant species, the African pouched mouse (Muroidea: Saccostomus campestris)
Rodents, despite their ecological importance, often receive little attention in conservation science. Among them, the South African pouched mouse (Saccostomus campestris) stands out as a generalist, omnivorous species inhabiting diverse environments across southern and central Africa. Its adaptability and ecological role make it an ideal model for exploring genetic diversity, population structure, and phylogenetic relationships. In this study, we developed critical genomic resources for S. campestris, focusing on both mitochondrial and nuclear DNA. Twelve novel Simple Sequence Repeat (SSR) markers were designed and validated, offering insights into population genetics and diversity. While heterozygosity and polymorphism rates were low overall, the markers proved robust for genetic studies. Notably, one SSR locus, SC9, displayed a null allele and deviated from the Hardy-Weinberg equilibrium, highlighting the unique genetic characteristics of the population. The complete mitochondrial genome (mtDNA) was assembled and assessed, showing evidence of heteroplasmy and some uncommon features like the use of alternative start and stop codons and an uncommon tRNA conformation. Using a mitogenomic approach the phylogenetic analysis reflected a closer placement of S. campestris to the Dendromurinae clade instead of Cricetomyinae. This work represents the first comprehensive genomic exploration of S. campestris, including the full mtDNA and a validated SSR panel. These tools lay the groundwork for future studies on genetic diversity, adaptation, and conservation strategies for this species and other underrepresented members of the family Nesomyidae. By contributing valuable genetic resources, we aim to advance the understanding of rodent biodiversity and its broader implications for ecosystem conservation and management.