Structure, functionality, and evolution of the BARE-1 retrotransposon of barley

The BARE-1 retrotransposon is a major, active component of the genome of ba rley (Hordeum vulgare L.) and other Hordeum species. Copia-like in its orga nization, it consists of 1.8-kb long terminal repeats bounding an internal domain of 5275 bp which encodes a predicted polyprotein of 1301 residues. T he polyprotein contains the key residues, structural motifs, and conserved regions associated with retroviral and retrotransposon GAG, aspartic protei nase, integrase, reverse transcriptase, and RNaseH polypeptides. BARE-1 is actively transcribed and translated. As part of our effort to understand th e evolution and function of BARE-1, we have examined its copy number and lo calization. Full-length members of the BARE-1 family constitute 2.8% of the barley genome. Globally, they are dispersed throughout the genome, excepti ng the centromeric, telomeric, and NOR regions. Locally, BARE-1 occurs more commonly in repetitive DNA than in coding regions, forming clusters of nes ted insertions. Both barley and other Hordeum genomes contain a high propor tion of BARE-1 solo LTRs. New techniques have been developed which exploit the insertion site polymorphism generated by -1 integration to produce mole cular markers for breeding, biodiversity, and mapping applications.