With thedevelopment of DNA sequencing techniques, more and more eukaryotic genomes aresequenced, assembled and annotated.  Nowwe know that many eukaryotic genomes are relatively large, extraordinarilyrepetitive and highly complicated.

  One questionthat remains is what evolutionary forces generate the complexity of eukaryotic genomes.  In this chapter, we discuss one of thepossible answers to this question: The mechanisms and evolutionary impacts oftransposable elements. Transposable elements (TEs or transposons) exist in mostof eukaryotic genomes. TEs are DNA sequences that can move from one genomic locationto another.  Transpositions of TEs caninduce diverse genome rearrangements such as deletion, inversion, duplicationand translocation.

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  Although sometimes TEsare called “junk DNA” because their activities are mostly silenced and difficultto detect, various studies have indicated that TEs have significantcontribution to shaping eukaryotic genomes and regulating gene expression. Differentfrom standard transposition which involves only one transposon, alternativetransposition involves at least two distinct TEs, undergoes more complicatedmovements and generates more significant genome structure variations.  Here we describe multiple alternative transposition events and illustrate a variety of genomerearrangements induced by transposable elements.  We highlight that TEs play an import role inthe process of genome evolution.