Transposable elements (TEs or transposons) are DNA sequences that can move from one genomic location to another, and they are highly represented in most eukaryotic genomes. TEs are often called “junk DNA” because most copies are silenced and have no obvious function; however, various studies have indicated that TEs have made major contributions to shaping eukaryotic genomes and regulating gene expression. In this presentation, I will show that TE transpositions can induce a variety of genome rearrangements including deletion, inversion, duplication and translocation especially the novel structure composite insertions. These occur as direct products of alternative transposition pathways. Unlike standard transposition which involves only one transposon, alternative transposition involves two distinct TEs, undergoes more complicated movements and generates more significant genome structure variations. In this presentation, I will also propose a new method of TIR element detection and annotation in maize genomes. This new pipeline cooperates the advantage of current annotation methods and the superiority of machine learning based method, thus this pipeline increased the efficiency and accuracy of TIR elements annotation. By getting a better annotation, we were able to analyze the patterns and impacts of TIR elements in maize genomes. Our study shows that the proportion of DNA elements is much larger than the estimation from current annotation in maize and the distribution of TIR elements correlated to the genome shape and these DNA sequences have impacts on genome evolution and contributed to maize genome diversity.