Dynamic Transposable Element Expression Across Development in Maize

Transposable elements (TEs) comprise a large portion of many eukaryotic genomes and are unique in their ability to replicate and move within the genome. The maize genome size is largely inflated by TE insertions, with the majority of these sequences derived from retrotransposons. While a handful of specific TE families have been well characterized in maize, the majority of TEs have been difficult to characterize due to challenges associated with annotating and mapping reads to the repetitive regions of many TE families. Maize TEs have been associated with transcriptional changes in nearby genes, however little is known about the expression dynamics and regulation of the TEs themselves. We have utilized a new structural annotation of maize TEs in combination with novel approaches to assess multi-mapped reads to perform whole-genome characterization of TE expression on a per-family basis. This methodology allows for the identification of families with variable expression across tissues and/or genotypes. We find substantial variation in the proportion of the transcriptome derived from TEs in different maize tissues. There is also evidence for many TE families with tissue-specific expression, suggesting dynamic control of TE expression during plant development.