Characterization of TSCL, a nonviral retroposon from Arabidopsis thaliana

We isolated by differential screening a 1.2 kb cDNA from an Arabidopsis thaliana ecotype Columbia cDNA Library that is highly expressed in stem and root. In situ hybridization studies on stem sections and root sections showed that the mRNA is expressed in stem sclerenchyma and root cortex, respectively. The isolation and sequence analysis of four other overlapping cDNA clones from two independent A. thaliana cDNA libraries confirmed that these cDNAs lack a significant open reading frame that has recognizable homology to any known proteins. We have obtained from A. thaliana ecotype Columbia three corresponding genomic clones and nucleotide sequence analysis of these clones revealed that we have isolated a retroposon, TSCL, that is flanked by two 13 bp direct repeats, is intronless, and has a poly(A)(+) tract at the 3' end. The site of transcription initiation mapped by primer extension analysis lies 48 bp downstream from an external TATA box. Results from Southern blot analysis suggest that TSCL occurs as a single-copy insert in the genomes of A. thaliana ecotype Columbia (Col-0) and Col-2 but is absent in the genomes of Brassica napus, Brassica juncea and A. thaliana ecotypes Be-0, Oy-0 and Ler-0. This suggests that Col-0 and Col-2 are phylogenetically more closely related to each other than to Be-0, Oy-0 and Ler-0, and that the Laibach Landsberg seeds Redei received, from which ecotypes Col-0, Col-2 and Ler-0 originated, were heterogeneous for TSCL.