Transposable element variation inferred from long-read sequences in wild house mice from temperate and tropical environments

Transposable elements (TEs) are a significant component of mammalian genomes, though their role in individual variation among natural populations has been largely unknown. Researchers have now utilized long-read whole-genome sequencing to explore TE variation in wild house mice (Mus musculus domesticus) from two distinct populations, one from a temperate environment and the other from a tropical environment.

Both groups were sampled, and highly contiguous de-novo genome assemblies were created for each mouse, enabling the identification of TEs absent from the standard mouse reference genome.

Manual TE curation led to the identification of 506 non-redundant TE consensus sequences across all mice. On average, each wild mouse genome contained approximately 1.47 million TE insertions, with around 4% of these insertions showing variation among individuals. A small percentage of these polymorphic TE insertions were notably more frequent in one population compared to the other, suggesting potential positive natural selection.

Through the analysis of liver RNA-seq data from natural populations and laboratory crosses, researchers examined gene expression in relation to polymorphic TEs. This investigation identified a small subset of TEs that are associated with the expression of nearby genes in a population-specific manner. Nearly all of these TEs exhibited independent signatures of positive selection, indicating their potential adaptive role in the environment.

These findings represent the first comprehensive assessment of TE variation in natural populations of house mice and highlight a small set of TE insertions that are likely to contribute to environmental adaptation.