Historical Dynamics of Transposable Elements in Herbarium Specimens of Arabidopsis thaliana Collected in Germany

Abstract

The dynamics of plant genomes under natural environmental conditions represent a compelling area of research. Among these, transposition events involving transposable elements (TEs) are of particular interest, as they can disrupt gene function or alter gene expression, thereby contributing to evolutionary processes and genetic diversity. This study investigated the transposition dynamics of TEs in Arabidopsis thaliana using whole-genome sequencing data derived from herbarium specimens collected in Germany, as provided by the dataset Historical Arabidopsis thaliana genomes from Germany. From 35 accessions, 331 terminal sequence pairs corresponding to transposed TEs were identified. Comparative analysis of TE transposition across individuals revealed evidence of hybridization among A. thaliana accessions collected over a 140-year period (1817–1957) across various regions of Germany. Transpositions specific to individual accessions were more prevalent than those shared among multiple accessions. Shared transpositions tended to occur more frequently between accessions that were geographically closer and collected within similar timeframes. Notably, cases of transposition that did not align with patterns expected from natural pollen dispersal were also detected. The TE detection method employed in this study, transposable element finder (TEF), proved effective for analyzing genome dynamics and offers a complementary perspective to traditional SNP-based diversity analyses using next-generation sequencing (NGS) data.