This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Transposable elements (TEs) play important roles in structural and functional diversification, genome enlargement, and speciation in plant genome. Their derivatives or small non-autonomous TEs play important roles in the alteration of homologous genes by epigenetic control or structural modification. The miniature inverted-repeat transposable element (MITE) is one of the representative non-autonomous class II TEs. MITEs include high copy members that are widely distributed and in close association with genic regions, which make MITEs useful targets and resources for in-depth understanding of genome evolution, as well as practical applications in molecular breeding. Here, we discuss the important features of MITEs, such as the identification tools of a novel MITE family, structural characterization, distribution pattern analysis, and impact on evolution in highly duplicated Brassica genome. We show the characteristics, copy numbers, and distribution patterns of 20 novel MITE families, and represent their putative roles in the evolution of the triplicated Brassica genome. We also introduce our MITE database, and discuss the utility of MITEs for developing MITE-derived markers that are useful for molecular breeding of Brassica crops.

Transposable elements occupy large portions of eukaryotic genomes and play an important role in genome evolution. Terminal repeat retrotransposons in miniature (TRIMs), short interspersed elements (SINEs) and miniature inverted-repeat transposable elements (MITEs) are representative forms of so-called miniature transposable elements (mTEs), which are present in very high-copy numbers, stable, widely distributed and in close association with genic regions in plant genomes. These features make mTEs useful for applications such as developing marker systems, functional characterization of associated genes, and elucidating the contribution of TEs to gene evolution. Here, we summarize the characteristics, copy numbers and distribution patterns of five TRIM families, 14 short interspersed elements (SINE) families and 20 MITE families in the Brassica rapa genome. We also show the comparative distribution pattern of paralogous mTE family members in Brassica oleracea and 11 B. rapa accessions. In addition, we describe putative roles for mTEs in the evolution of the triplicated Brassica genome and discuss the utility of mTEs for analysis of genome evolution and for developing practical marker systems.