The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

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.