Single integration and spread of a Copia-like sequence nested in rDNA intergenic spacers of Allium cernuum (Alliaceae)

Abstract

The 35S ribosomal DNA (rDNA) intergenic spacer (IGS) of Allium cernuum is examined. Initial sequencing of IGS clones revealed that some rDNA units contain a truncated retrotransposon sequence most similar to members of the Copia superfamily. Fluorescence in situ hybridisation (FISH) to metaphase chromosomes indicates that this element is dispersed along both pairs of major rDNA arrays. Southern hybridisation confirmed the presence of this 'relic' Copia-like element in more than 10% of 35S rDNA units, in the same position within the IGS. To measure the intragenomic divergence of the relic retroelement and its flanking sequences amongst different rDNA units, a 1.1-kb region was amplified and cloned. These data collectively point to a single origin for units containing the putative retrotransposon fragment. It is likely that units containing the putative retroelement increased in copy number and dispersed via rDNA homogenisation mechanisms, rather than by multiple retrotransposition events.