Genome-Wide Analysis of Transposable Elements in the Barley Genome.

Barley (Hordeum vulagare L.) is a model plant in genomic studies of Triticeae species. However, as with other Triticeae species, it has a large (5.1 Gb) complex genome with a high fraction of repetitive sequences. Majority of the barley genome (~84%) is composed of transposable elements (TEs). Characterization of TEs provides a view of the barley genome structure. TEs change their location within the genome by “copy-and-paste” or “cut-and-paste” mechanisms. The movement of TEs within the genome generates unique repeat junction (RJ) consisting of the TE boundaries and the sequences in which they land. We investigated RJ sequences for the genome-wide analysis of TEs. Using 10.2 Gb of the barley survey sequencing data, 981,561 RJs were detected by “RJPrimers” pipeline. Subsequently, we developed a script to identify TEs based on the detected RJs. We identified 1,190,885 TEs that were distributed evenly across all seven barley chromosomes. Two TE superfamilies, Gypsy and Copia, had the highest copy numbers representing ~86% and ~21% of TEs, respectively. Also, the RJs analysis revealed that the insertion of TEs within the genome is not random and that the majority of TEs have preferential insertion sites. Based on this finding we propose that during evolution amplification of TE preferential target sites triggered the amplification of inserted TEs and led to the burst of TE copy numbers in the Triticeae genome. The results of this study show that analysis of RJ sequences is a powerful tool for detecting TEs and studying their insertion pattern, especially for the species for which the complete genome sequence is not available.