BARE-ID, a representative of a family of BARE-like elements of the barley genome.

In our search for transposable elements in barley, Hordeum vulgare, we have isolated and cloned two BamHI-fragments of 4.7 and 4.2 kb in length containing very abundant DNA sequences. The 4.7 kb fragment is homologous to the extended region, including more than half of the 5'-LTR and some part of the coding domain of BARE-1, a member of copia-like retrotransposon family of barley. The 4.2 kb fragment, bearing homology to BARE-1 and the WIS-2 family isolated from wheat, is unique among studied retroelements of cereals because it consists of two inverted parts, each containing homology to the LTR and UTL of BARE-1. Functional motifs for reverse transcription, two TATA-boxes and two primer-binding sites, were found within the LTRs. The element contained within this fragment was generated by significant rearrangement of a BARE-like retrotransposon, which included inversion of the extended 5'-terminal region and deletion of the internal domain. Therefore this element is named BARE-ID (BARE-inverted, deleted). A family of BARE-like elements is amplified in the H. vulgare genome compared with wild barley species. The terminal inverted repeat of BARE-ID was used as a probe for examination of evolutionary diversity within genus Hordeum. Our data are basically in agreement with the modern classification system. However, they do not support the combination of H. vulgare and H. bulbosum into one group with the same type of genome. New data concerning the possible origin of the polyploid species, H. secalinum, confirm that retrotransposons are a useful tool for phylogenetic studies.