The genome of many plant species is composed of genes interspersed in large regions of intergenic space containing large stretches of transposable elements (TEs). While TEs contribute only a small proportion of the transcriptome, TE transcription is dynamic across development, stress, and in variable genotypes. Understanding the dynamics of TE transcription improves understanding of how genomes are regulated. Furthermore, some TEs can act to regulate the expression of nearby genes, and detailed analysis of transcriptome dynamics in a TE-aware manner will improve our understanding of how regulatory novelty arises in genomes.