A high-resolution computer-based survey for transposable elements performed on 910 Kb of rice genomic DNA sequences revealed the presence of both class I and class II transposable elements. Elements from most major families of plant transposable elements were identified, and new groups were reported for these families. Miniature inverted-repeat transposable elements (MITES) are clearly the predominant type of transposable element in the rice sequences examined. Phylogenetic analysis of the putative transposases of several transposable elements indicated that Tourist-like miniature inverted-repeat transposable elements (MITES) are closely related to the bacterial insertion sequence 5 (IS5) family of transposable elements, while Emigrant-like and Stowaway-like MITES are both related to members of the IS630/TcI/mariner superfamily of elements. Finally, the nucleotide sequences of MITES, Ac-like, Mutator-like elements (MULE), short interspersed nuclear elements (SINEs) and other unclassified elements, as well as their insertion polymorphism data have been used to reconstruct the relationships between rice species in the AA genome. The use of a combination of transposable element data sets generated the most reliable cladograms.

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