Characterization of the PIF/Pong superfamily of DNA transposons and their relationship with tourist-like miniature inverted-repeat transposable elements (MITEs)
MetadataShow full item record
Transposable elements (TEs) are ubiquitous in the genomes of all organisms characterized to date and are major components of plant genomes. The two classes of TEs, class 1 (RNA) and class 2 (DNA) elements, are distinguished by their transposition intermediate. DNA elements are further classified into superfamilies based on homology in the transposases catalyzing their transposition. Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements widespread and abundant in plants and animals. Because MITEs lack coding capacity, their origin and transposition mechanism remained largely unknown. The researches described in this dissertation were directed to understand the origin and transposition mechanism of Tourist-like MITEs. Chapter 2 describes the identification of a Tourist-like MITE family (mPIF) and the characterization of an active DNA element family, P Instability Factor (PIF) in maize (Zea mays). Significant similarities shared by PIF and mPIF elements indicate mPIF MITEs are nonautonomous members of the PIF family. Identification of a transposase-encoding PIF element (PIFa) through genetic analysis led to the discovery of a new superfamily of DNA elements (called PIF/Pong) widespread in eukaryotes. These results indicate that members of the PIF/Pong superfamily are responsible for the origin and amplification of Tourist-like MITEs. Chapter 3 characterizes the PIF/Pong superfamily with regard to its distribution, evolution and relationship with Tourist-like MITEs. A comprehensive survey identified hundreds of PIF/Pong-like transposases from plants, animals and fungi, and the evolutionary relationships of these transposases were examined through phylogenetic analyses. Relationships between PIF/Pong-like elements and Tourist-like MITEs were investigated in rice (Oryza sativa), where the vast majority of Tourist-like MITEs was found related to PIF/Pong-like elements. Chapter 4 was directed to understand the contribution of TE proliferation to the genome size expansion of Brassica oleracea and the cause for the low TE content of the Arabidopsis genome. The TE diversity, abundance and phylogeny of Arabidopsis and B. oleracea were compared. The results indicate that the amplification of both class 1 and class 2 TEs contributed significantly to the B. oleracea genome size expansion and that reduced TE proliferation is largely responsible for the low TE content and small genome size of Arabidopsis.