TREP: a database for Triticeae repetitive elements

Wading through the quagmire of repetitive sequences can be a difficult and uninspiring task, and frequently, only PCR fragments of conserved domains in repetitive elements (e.g. sequences encoding reverse transcriptase) are available.

Abstract

Genomes of the important crop plants wheat, barley and rye are large (5 × 109 to 17 × 109 bp) and contain 80% repetitive sequences. Although research on the molecular genetics of Triticeae concentrates on gene-rich regions, most genomic and some EST sequences isolated from these species are repetitive. Rapid identification of repetitive elements could significantly speed up the process of gene discovery and chromosome walking. Unfortunately, wading through the quagmire of repetitive sequences can be a difficult and uninspiring task. Classification and naming of such elements has been somewhat arbitrary and occasionally the same elements have even been classified and named differently by different researchers (e.g. 'Sabrina' [ 1. Shirasu K. et al. A contiguous 66 kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 2000; 10: 908-915 Crossref PubMed Scopus (273) Google Scholar ] and 'XA' [ 2. Wicker T. et al. Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 2001; 26: 307-316 Crossref PubMed Scopus (201) Google Scholar ]). Often, repetitive elements are not present as complete copies but are fragmented by the insertion of other elements or by deletions, adding to the complexity of the analysis. In addition, frequently, only PCR fragments of conserved domains in repetitive elements (e.g. sequences encoding reverse transcriptase) are available.