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 distributedsigmodontine rodent that inhabits a broad range of environments, from the hyper ariddeserts of southernmost Perú and northern Chile to the Patagonian steppe to the humidtemperate rainforests of southern South America. Its extensive ecological breadth, coupledwith physiological adaptations to water scarcity, makes it an ideal model for studyingenvironmental responses and phenotypic plasticity. Here, we present the first de novoscaffold-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 completenessscore of 98.61%, indicating high sequence completeness. Genome annotation identified21,476 protein-coding genes, providing a valuable resource for evolutionary, ecological, andfunctional genomics. As a case study, we used this reference genome to explore geneexpression and genetic divergence in kidney tissue from individuals inhabiting contrastingenvironments: the southern Andean rainforest and the Patagonian steppe. By integratingsingle-cell transcriptomic data from Mus musculus, we performed cell type deconvolution,revealing environment-specific expression patterns linked to renal function. This newgenomic resource opens avenues for investigating local adaptation, population structure,and conservation genetics in one of South America´s most ecologically versatile and widelydistributed rodents.