Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii

摘要: Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on host genomes range from an extensive size variation to regulation of gene expression, altering function and creating new genes. Because TEs pivotal contribute genome structure regulation, their identification characterization provide a wealth useful data gaining in-depth understanding functioning. The giant reed (Arundo donax) is perennial rhizomatous C3 grass, octadecaploid, with estimated nuclear 2744 Mbp. It promising feedstock second-generation biofuels biomethane production. To identify characterize repetitive in A. donax its ancestral plinii species, we carried out low-coverage whole shotgun sequencing both species. Using de novo repeat approach, 33,041 28,237 non-redundant sequences were identified characterized genomes, representing 37.55 31.68% each genome, respectively. Comparative phylogenetic analyses, including major TE classes plinii, together rice maize paralogs, understand evolutionary relationship classes. Highly conserved copies RIRE1-like Ty1-Copia discovered two Arundo spp. which they represented nearly 3% genomic sequence. We medium/highly unexplored polyploid thus generating information study structure, composition, functioning these non-model provided valuable resource that could be exploited any effort aimed at assembling