Arguments for standardizing transposable element annotation in plant genomes

•Transposable elements contribute to epigenetics and non-Mendelian inheritance.•Genomic stress triggers transposon activity resulting in epigenetic novelties.•Transposable element annotation strategies in draft genomes need standardization.•Standardized annotation of transposable elements will help comparative genomics.

Whole genome sequence assemblies have been generated for many plants. Annotation of transposable elements (TEs), which constitute the major proportion of genomes and play a significant role in epigenome alterations under stress, has not been given equal importance to that of genes. In this opinion article, we argue that the lack of focus dedicated to the fine-scale characterization of repeat fractions and the absence of consistent methods for their annotation impede our ability to critically understand the influence of TEs on the epigenome with implications in gene expression and non-Mendelian inheritance. Major structural changes occur over an evolutionary time scale. However, epigenetic regulation mediated by TEs can happen in a single generation, thus emphasizing the need for their standardized annotation.