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 families and superfamilies based on homology in the transposases catalyzing their transposition.;The researches described in this dissertation were directed to understand the evolutionary dynamics of two closely related families of DNA TEs, PIF and Pong, in Triticeae genomes. Phylogenetic analysis of numerous PIF and Pong-like transposase sequences revealed that both groups of elements are widely dispersed within the Triticeae genomes and they appear to have shared similar evolutionary trajectory within the tribe, best explained by the existence of diverse ancestral transposase lineages that were vertically transmitted, with some lineages experiencing differential evolutionary success, and occasional horizontal transfer between genera. However, both groups of elements display unique features and vary considerably in their transcriptional activity. No Pongrelated transcripts were detected, while an abundance of PIF related transcripts were identified in all Triticeae accessions, indicating wide variation in the activity of closely related TEs within the same genome. The analysis of PIF cDNA transcripts revealed that multiple distinct transposase lineages have remained transcriptionally competent during the long evolution of the tribe.