Comparative Analysis of Repeat Landscapes in Avena (Oat)

Avena sativa, or common oat, is a staple crop and member of the Poaceae or Grasses family. Following behind wheat, maize and rice, oats account for 10.5 million hectares of the world’s produced crops as of 2017. Phytocompounds such as β-glucan and other phytochemicals such as avenanthramides, vanillic, syringic, ferric, and caffeic acids are noted to benefit cardiovascular health or represent prospective benefactors to human health, however further investigation into these potential benefiting factors requires research that surpasses past works in breadth and scope. Much has been done to bridge the gap in resources for oats, such as the development of high throughput markers, consensus linkage maps and most recently genome sequencing efforts, however the relative complexity of cultivated oat, an allohexaploid with high similarity subgenomes, provides additional challenges to the development of these resources. A final layer of complexity is the genome size of hexaploid oats, believed to be approximately 12.8 gigabases, of which a significant portion is composed of complex repetitive elements. Characterization of these highly complex repetitive regions is difficult as repetitive regions contained within reads are characteristically difficult to map, thereby complicating assembly efforts and resulting in misassembly and gaps. Through investigation of repetitive elements by utilization of a novel pipeline capable of offering enhanced resolution and detection of repetitive elements, use of this novel information of all repetitive elements in a given genome were further examined within well-characterized Avena genomes, concluding with phylogenetic analyses examine evolutionary relationships between elements in efforts to gain insight into the of the role transposable elements across Avena, and bolster overall knowledge of the Avena family.