BARE-1 INSERTION SITE PREFERENCES AND EVOLUTIONARY CONSERVATION OF RNA AND CDNA PROCESSING SITES

The BARE-1 copia-like retrotransposon constitutes nearly 7% of the bar ley (Hordeum vulgare L.) genome as a family of more than 2 x 10(4) mos tly full-length copies dispersed on all chromosomes. BARE-I elements a re transcribed in barley tissues from promoters within the LTR (long t erminal repeat). The predicted, translated polyprotein contains conser ved domains for GAG, aspartic proteinase, integrase, reverse-transcrip tase, and RNase H. Here, we have used inverse PCR with LTR-based prime rs to establish the consensus sequences for the terminal region of the LTR, the external dinucleotides of the cDNA integration intermediate, and the minus-and plus-strand priming sites. These key functional ent ities are well-conserved in the BARE-1 family, including wheat Wis2, b ut differ from those of other plant retrotransposons. The target site duplication was established as 5 bp. Of the 13 integration sites ident ified here, 8 were other BARE-1 elements and 1 another retrotransposon ; 59% of the total 17 identified BARE-1 insertion sites are retrotrans posons. This nested insertion pattern may represent a basic feature of plant retrotransposons.