Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

Background – Structural differences between genomes are a major source of
genetic variation that contributes to phenotypic differences. Transposable
elements, mobile genetic sequences capable of increasing their copy number
and propagating themselves within genomes, can generate structural
variation. However, their repetitive nature makes it difficult to
characterize fine-scale differences in their presence at specific
positions, limiting our understanding of their impact on genome variation.
Domesticated maize is a particularly good system for exploring the impact
of transposable element proliferation as over 70% of the genome is
annotated as transposable elements. High-quality transposable element
annotations were recently generated for de-novo genome assemblies of 26
diverse inbred maize lines. Results – We generated base-pair resolved
pairwise alignments between the B73 maize reference genome and the
remaining 25 inbred maize line assemblies. From this data, we classified
transposable elements as either shared or polymorphic in a given pairwise
comparison. Our analysis uncovered substantial structural variation
between lines, representing both putative insertion and deletion events.
Putative insertions in SNP-depleted regions, which represent recently
diverged identity by state blocks, suggest some TE families may still be
active. However, our analysis reveals that genome-wide, deletions of
transposable elements account for more structural variation than
insertions. These deletions are often large structural variants containing
multiple transposable elements. Conclusions – Combined, our results
highlight how transposable elements contribute to structural variation and
demonstrate that deletion events are a major contributor to genomic
differences.