Mining of Repetitive Sequences from Eragrostis tef var Enatite Genome

Eragrostis tef (Zucc.) Trotter, an orphan crop, is the major cereal crop originated and widely cultivated in Ethiopia where it provides nutrition for more than 50% of the population. Tef belongs to the Poaceae and is an allotetraploid (2n= 4x = 40) with a nuclear genome size of 730 Mbp. It is rich in essential amino acids, minerals (particularly Fe and Ca) and it is gluten free. Low coverage genomic DNA sequencing data were generated from E .tef var Enatite seedlings in order to characterize the repetitive component of tef using a range of de novo repeat identification tools. Search for similarity and structural features were then carried out to fully characterize the medium/highly abundant repetitive elements paying particular attention to Transposable Elements (TEs). TEs play major role in shaping eukaryote genome structure and are responsible for causing mutation, genome size variation, chromosomal rearrangements, gene regulation and inactivation, exon reshuffling. A library including 1389 medium/highly repetitive sequences estimated to represents about 27% of the Tef genome was isolated. Ty3-gypsy (11.4%) found to be the more abundant component of LTR-retrotransposons than Ty1-copia (2.67%). Phylogenetics analyses of the most important classes of TEs were carried out by extracting paralogous elements from tef, rice and maize. Finally, a previously undetected satellite sequence, which covers more than 4% of the whole genome, was identified and partially characterized.