Aside from polyploidy, transposable elements are the major drivers of genome 
size increases in plants. Thus, understanding the diversity and evolutionary 
dynamics of transposable elements in sunflower (Helianthus annuus L.), 
especially given its large genome size (∼3.5 Gb) and the well-documented cases 
of amplification of certain transposons within the genus, is of considerable 
importance for understanding the evolutionary history of this emerging model 
species. By analyzing approximately 25% of the sunflower genome from random 
sequence reads and assembled bacterial artificial chromosome (BAC) clones, we 
show that it is composed of over 81% transposable elements, 77% of which are 
long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon 
fraction in BAC clones harboring genes is disproportionately composed of 
chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the 
majority of the intact chromoviruses contain tandem chromodomain duplications. 
We show that there is a bias in the efficacy of homologous recombination in 
removing LTR retrotransposon DNA, thereby providing insight into the mechanisms 
associated with transposable element (TE) composition in the sunflower genome. 
We also show that the vast majority of observed LTR retrotransposon insertions 
have likely occurred since the origin of this species, providing further 
evidence that biased LTR retrotransposon activity has played a major role in 
shaping the chromatin and DNA landscape of the sunflower genome. Although our 
findings on LTR retrotransposon age and structure could be influenced by the 
selection of the BAC clones analyzed, a global analysis of random sequence reads 
indicates that the evolutionary patterns described herein apply to the sunflower 
genome as a whole.