Zea ribosomal repeat evolution and substitution patterns

Zea and Tripsacum nuclear ribosomal internal transcribed spacer (ITS)sequences were used to evaluate patterns of concerted evolution, rates ofsubstitutions, patterns of methylation-induced deamination, and structuralconstraints of the ITS. ITS pseudogenes were identified by theirphylogenetic position, differences in nucleotide composition, extensivedeamination at ancestral methylation sites, and substitutions resulting inlow-stability secondary RNA structures. Selection was important in shapingthe kinds of polymorphisms and substitutions observed in the ITS. ITSsubstitution rates were significantly different among the Zea taxa.Deamination of cytosines at methylation sites was a potent mutation source,but selection appeared to maintain high methylation site density throughoutthe ribosomal repeat except for the gene promoter. Nucleotide divergencestatistics identified selectively constrained regions at the 5' ends of theITS1 and ITS2.