Miniature transposable elements (mTEs): Impacts and uses in the Brassica genome

Abstract

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.