The Repetitive Landscape of the Barley Genome

Most plant genomes are so large, with a mean mean size of over 5,600 Mb (1), that animal genomes are dwarfed by comparison. Although transposable elements (TEs) comprise the majority of DNA in large plant genomes, it is poorly understood how TEs shape genomes and contribute to their evolution. Here we present an analysis of the repetitive fraction of the 5,000 Mb barley genome, which is the first actually “normal-sized” plant genome sequenced. Only about 2% of the genome is gene space, while the rest is overwhelmingly comprised TE-derived sequences. Interestingly, we found that the barley genome is highly compartmentalized with different types of TEs occupying different “niches” within the genome. Their evolutionary history and genetic makeup seems to enable them to specifically target their preferred genomic region. Different families of large elements (e.g. retrotransposons) show a variety of preferences for different chromosomal locations such as telomeres, centromeres or central parts of chromosome arms. Interestingly, gene space is its own distinct genomic compartment which is enriched in small non-autonomous DNA transposons. The latter have evolved to specifically target promoters and downstream regions of genes. Furthermore, we found evidence that insertions of TEs in promoter regions of genes may be part of a feedback mechanism that prevents regulatory regions from being methylated. In summary, the near-complete genome sequence of barely has revealed a broad inside into dynamics and evolution of TEs in a large plant genome.