Incomplete homogenization of 18 S ribosomal DNA coding regions in Arabidopsis thaliana

BACKGROUND: As a result of concerted evolution, coding regions of ribosomal DNA sequences are highly conserved within species and variation is generally thought to be limited to a few nucleotides. However, rDNA sequence variation has not been systematically examined in plant genomes, including that of the model plant Arabidopsis thaliana whose genome was the first to be sequenced. FINDINGS: Both genomic and transcribed 18 S sequences were sampled and revealed that most deviation from the consensus sequence was limited to single nucleotide substitutions except for a variant with a 270 bp deletion from position 456 to 725 in Arabidopsis numbering. The deletion maps to the functionally important and highly conserved 530 loop or helix18 in the structure of E. coli 16 S. The expression of the deletion variant is tightly controlled during developmental growth stages. Transcripts were not detectable in young seedlings but could be amplified from RNA extracts of mature leaves, stems, flowers and roots of Arabidopsis thaliana ecotype Columbia. We also show polymorphism for the deletion variant among four Arabidopsis ecotypes examined. CONCLUSION: Despite a strong purifying selection that might be expected against functionally impaired rDNAs, the newly identified variant is maintained in the Arabidopsis genome. The expression of the variant and the polymorphism displayed by Arabidopsis ecotypes suggest a transition state in concerted evolution.