Mutation followed by selection is the basis for evolution and drives diversification. These mutations can be small single nucleotide changes or larger insertions or deletions of DNA sequence, referred to as structural variants. Structural variation is often associated with the repetitive nature and functional activity of transposable elements. Here, we used whole genome alignments to identify structural variation between the maize reference genome and 25 other inbred maize lines. We intersected these genomic structural variants with publicly available transposable element annotations to determine what proportion of the structural variation is annotated as transposable element. The make-up of transposable elements at each structural variant allowed us to predict whether the variant represented a likely insertion or deletion event. We find that many variants are likely deletion events composed of multiple transposable element types, as well as sequence that did not originate from a transposable element. Our results demonstrate the role that transposable elements play in generating genomic diversity and provide a valuable resource for future studies of diversity across transposon-rich maize genomes.
