The publication of the B73 maize reference genome assembly in 2009 was a monumental achievement and marked an important milestone in the field of maize genetics. This resource has been pivotal to countless discoveries since its release. One of the most surprising of these discoveries, however has been the finding that many sequences are missing or significantly diverged from the reference genome. This realization has helped spur the generation of alternative maize reference genome assemblies including one for the elite inbred line, PH207. The first chapter in this work provides a detailed historical perspective of the study of structural variation in maize and presents a review of the current understanding of the maize pan-genome. The middle chapter consists of original research using the PH207 reference genome to understand the significance of differential fractionation to the prevalence of structural variation in maize. The third chapter explores the contribution of transposable elements to variation in the maize transcriptome. Together these sections highlight the importance of using multiple maize reference genomes to understand the extraordinary diversity in the maize genome and point towards the need for a nuanced and contextualized understanding of this sequence diversity.