Navigating the Maze of Maize Genomics: The Impact of Transposable Elements and Tandem Repeats

Transposable elements (TEs) are abundant and ubiquitous components of eukaryotic genomes. Since TEs were first discovered in maize (<i>Zea mays</i>) by Barbara McClintock in the late 1940s, these elements have been shown to be important agents in shaping genome structure and evolution. Today, maize continues to be an important model organism for molecular and quantitative genetics, and represents a particularly useful system for the study of the interplay between TEs and host genomes. While TEs constitute a significant part of the maize genome and are important drivers of genome evolution, their annotation remains a complex and challenging task. Here, we discuss genome annotation of TEs and other repetitive sequences in maize genomes. We briefly review current knowledge on the overall landscape of TE and non-TE repeats in maize, and discuss how these sequences may impact genome structure, and the genotype and phenotype within species. We also provide a summary of the main tools used to find TE polymorphisms, and briefly introduce four different bioinformatic approaches for TE and tandem repeat annotation, explaining how they can be best used by maize researchers.