Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes

Abstract

Abrothrix olivacea (Waterhouse, 1837), the olive grass mouse, is a widely distributed sigmodontine rodent that inhabits a broad range of environments, from the hyper arid deserts of southernmost Peru and northern Chile to the Patagonian steppe to the humid temperate rainforests of southern South America. Its extensive ecological breadth, coupled with physiological adaptations to water scarcity, makes it an ideal model for studying environmental responses and phenotypic plasticity. Here, we present the first de novo scaffold-level genome assembly of A. olivacea, generated from short-read DNA sequencing. The 2.25 Gb assembly achieved a scaffold N50 of 123 Mb and a BUSCO completeness score of 98.61%, indicating high sequence completeness. Genome annotation identified 21,476 protein-coding genes, providing a valuable resource for evolutionary, ecological, and functional genomics. As a case study, we used this reference genome to explore gene expression and genetic divergence in kidney tissue from individuals inhabiting contrasting environments: the southern Andean rainforest and the Patagonian steppe. By integrating single-cell transcriptomic data from Mus musculus, we performed cell type deconvolution, revealing environment-specific expression patterns linked to renal function. This new genomic resource opens avenues for investigating local adaptation, population structure, and conservation genetics in one of South Americas most ecologically versatile and widely distributed rodents.