CRYPTIC SEQUENCE SIMPLICITY, NUCLEOTIDE COMPOSITION BIAS, AND MOLECULAR COEVOLUTION IN THE LARGE SUBUNIT OF RIBOSOMAL DNA IN PLANTS - IMPLICATIONS FOR PHYLOGENETIC ANALYSES

Sequences of the large subunit (LSU) of ribosomal DNA from Arabidopsis thaliana, Brassica napus, Sinapsis alba, Oryza sativa, Fragaria x ana nassa, Lycopersicon esculentum, and Citrus limon were analyzed for nuc leotide composition, presence of ''cryptic'' sequence simplicity, and evidence of molecular coevolution among the 12 expansion segments. The median value for GC content across the seven plants for the LSU was 5 6%, but the distribution of GC was nonrandom. Expansion segments were decidedly more GC rich (65% on average) than were the conserved core r egions (52% on average). Only Oryza sati va had significant cryptic se quence simplicity, which was found to be greatest in expansion segment s D8 and D12. Sequence similarity between expansion segments also was strongest in rice as determined by visual inspection of dot plots. The complex nature of sequence variation in the LSU of rDNA complicates t he use of this molecule as a molecular systematic marker.