With the
development of DNA sequencing techniques, more and more eukaryotic genomes are
sequenced, assembled and annotated.  Now
we know that many eukaryotic genomes are relatively large, extraordinarily
repetitive and highly complicated.  One question
that remains is what evolutionary forces generate the complexity of eukaryotic genomes.  In this chapter, we discuss one of the
possible answers to this question: The mechanisms and evolutionary impacts of
transposable elements. Transposable elements (TEs or transposons) exist in most
of eukaryotic genomes. TEs are DNA sequences that can move from one genomic location
to another.  Transpositions of TEs can
induce diverse genome rearrangements such as deletion, inversion, duplication
and translocation.  Although sometimes TEs
are called “junk DNA” because their activities are mostly silenced and difficult
to detect, various studies have indicated that TEs have significant
contribution to shaping eukaryotic genomes and regulating gene expression. Different
from standard transposition which involves only one transposon, alternative
transposition involves at least two distinct TEs, undergoes more complicated
movements and generates more significant genome structure variations.  Here we describe multiple alternative transposition events and illustrate a variety of genome
rearrangements induced by transposable elements.  We highlight that TEs play an import role in
the process of genome evolution.