Transposable Element Proliferation and Genome Size Evolution in Asparagales

Asparagales is an order of flowering plants including many important edible (asparagus, onion, tequila agave) and ornamental (orchid, amaryllis, aloe) species. Despite representing wide variation in karyotype and genome size, little is known about what constitutes the high proportion of repetitive sequences in genomes of Asparagales species. Genome sequencing is becoming a routine procedure to obtain data for many organisms, including molecular phylogenetic studies of various plant groups. The first step of these studies, however, is masking all repetitive elements. I utilized anonymous, low coverage, genome survey sequences (GSS) for a sample of species across Asparagales and applied a de novo genome assembly program. Given the low genome coverage, a majority of the resulting scaffolds represent plastome, mitogenome, and repetitive sequences. I summarized the scaffolds representing repetitive sequences to characterize the types of repetitive elements present in each genome, and mapped the raw reads back to the scaffolds to obtain estimates of abundance. The scaffolds represent both fragmented and complete sequences for a variety of transposable elements, including LTR retrotransposons, LINEs, SINEs, and DNA transposons. Quantification estimates indicate even closely related species possess different proportions of transposable elements in their genomes, suggesting genome size changes result from proliferative activity in a variety of repeat types.