Evolutionary Dynamics of PIF and Pong-like Transposable Elements in Triticeae

Transposable elements (TEs) are mobile genomic units with the ability to invade genomes through a process called transposition. The two classes of TEs, Class I (RNA) and Class II (DNA) elements, are distinguished by their transposition intermediate. DNA elements can further be classified into superfamilies based on homology in the transposases catalyzing their transposition. The researches described in this dissertation were directed to understand the evolutionary dynamics of PIF and Pong-like DNA TEs in Triticeae genomes. Chapter II describes the distribution and evolution of Pong-like TEs in the genomes of 21 diploid Triticeae species. A phylogenetic analysis of nearly 300 Pong sequences based on a conserved region of the transposase domain revealed complex evolutionary history of Pong elements that can be best explained by ancestral polymorphism followed by differential evolutionary success of some transposase lineages, and by occasional horizontal transfer between phylogenetically distant Triticeae genera. Chapter III examines the abundance and structural diversity of the Pong-like transposase gene in the genomes of 31 diploid Triticeae accessions, using transposon display. The results revealed varying levels of Pong proliferation in different genomes, with transposase copies ranging from 22 to 92. Comparative analysis of Pong transposase abundance to flow cytometry estimates of Triticeae genome size revealed that larger genomes were not correlated with increased Pong transposase abundance. Chapter IV describes the distribution and evolution of PIF-like elements in the genomes of Triticeae species. A phylogenetic analysis of 240 PIF sequences based on the conserved region of the transposase domain revealed al least four main transposase groups. In addition, 127 sequences with features of functional genes were identified, indicating possible recent activity of PIF. The results revealed complex evolutionary diversity of PIF elements that can be best explained by a combination of vertical transmission with some lineages experiencing differential evolutionary success, and occasional horizontal transfer events between phylogenetically distant genera. Chapter V was directed to survey for PIF- and Pong-related transposase activity in 13 diploid Triticeae species all of which have been shown to harbor extensive within-genome diversity of both groups of elements. The results revealed that PIF elements are actively transcribed in Triticeae. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic transposase sequences revealed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. No transcriptional activity of Pong elements was detected in any sample.