LINEs and gypsy-like retrotransposons in Hordeum species

LINE and gypsy-like retroelements were studied in the genome of Hordeum vulgare, and compared with the representatives of the major sections of the genus Hordeum. We isolated reverse transcriptase (RT) genes from four gypsy-like and three LINE families using PCR primers specific for the corresponding conserved domains. A full-length barley LINE of 6295 bp, named BLIN, was isolated from a BAC genomic library. BLIN looks alien in the barley genome because its G+C content is 62% compared to an average of 45%. The BLIN nucleotide sequence showed it was structurally intact with the features typical of non-LTR retrotransposons, including 16 bp target site duplications, two short cysteine motifs, and two degenerate open reading frames (ORFs). The high degeneracy was also found in RT domain of both gypsy-like and, particularly, LINE families. The copy numbers of the gypsy-like families were relatively low compared to well-characterized copia-like element BARE-1. Each gypsy-like family gave unique RFLP patterns when hybridized to genomic DNA from each of the four basic Hordeum genomes. H. vulgare (I genome) had accumulated more copies than the wild Hordeum species (H, X, Y genomes), with the other I genome species, H. bulbosum, being intermediate. Analysis of the BAC library and in situ hybridization with LINE RT domains showed the low copy number of the LINE families, but there was little correlation between hybridization patterns and the division of the genus into four basic genomes. The distribution and content of gypsy retrotransposons in the BAC library indicated that a few copies are nested, although most are present as single, distinct, copies. Our results suggest that the major groups of retroelements make individual contributions to the shape of the plant genome; the factors involved in their amplification and distribution are independent, also varying among species.