Characterization of chromosome-specific genomic DNA from hexaploid oat

We have sequenced, assembled, and characterized a set of complexity-reduced genomic clones derived from a chromosome 18D-specific library from hexaploid oat ( Avena sativa L.). Sequences from 314 clones were assembled into 99 contigs of identical or nearly identical sequence. The Censor tool was used to identify similarity to known and characterized repeat sequences in RepBase. Eight repeat classes were scattered throughout 50 contigs, with most repeats belonging to seven transposon and retrotransposon classes. After accounting for known repeats, additional matches to orthologous genes from other species were identified in 24 regions of 22 contigs, and an additional 47 regions matched genomic sequences from oat and other related species. These results provide information about the types and density of transposable elements in the oat genome, as well as the potential for identifying unique or chromosome-specific sequence elements in oat. Overall, these results predict a low success rate in identifying chromosome-specific coding regions in oat through chromosome isolation and genome complexity reduction.