The Au family, a novel short interspersed element (SINE) from Aegilops umbellulata

A novel plant short interspersed nuclear element (SINE) was identified in t he second intron of the acetyl CoA carboxylase gene of Aegilops umbellulata which has been designated "Au", for the host species in which it was disco vered. Au elements have a tRNA-related region, direct flanking repeats, and a short stretch of T at the 3' end, which are features common to Au and pr eviously characterized SINEs. Au elements are detected in the genomes of se veral monocots and dicots by DNA dot hybridization and are also found in th e tobacco genome by database searching. Au elements are present at an espec ially high copy number (approximately 10(4) copies per haploid genome) in w heat and Ae. umbellulata. This suggests a recent amplification of Au in the Triticum and Aegilops species. In situ hybridization revealed a dispersed distribution of Au elements on wheat chromosomes. Au elements were amplifie d by PCR from monocot and dicot species and the phylogenetic relationships among Au elements were inferred. This phylogenetic analysis suggests amplif ication of Au elements in a manner consistent with the retrotransposon mode l for SINE dispersion. The high copy number of Au elements and their disper sed distribution in wheat are desirable characteristics for a molecular mar ker system in this important species.