The phylogenetic potential of entire 26S rDNA sequences in plants

18S ribosomal RNA genes are the most widely used nuclear sequences forphylogeny reconstruction at higher taxonomic levels in plants. However, dueto a conservative rate of evolution, 18S rDNA alone sometimes provides toofew phylogenetically informative characters to resolve relationshipsadequately. Previous studies using partial sequences have suggested thepotential of 26S or large-subunit (LSU) rDNA for phylogeny retrieval attaxonomic levels comparable to those investigated with 18S rDNA. Here weexplore the patterns of molecular evolution of entire 26S rDNA sequencesand their impact on phylogeny retrieval. We present a protocol for PCRamplification and sequencing of entire (approximately 3.4 kb) 26S rDNAsequences as single amplicons, as well as primers that can be used foramplification and sequencing. These primers proved useful in angiospermsand Gnetales and likely have broader applicability. With these protocolsand primers, entire 26S rDNA sequences were generated for a diverse arrayof 15 seed plants, including basal eudicots, monocots, and higher eudicots,plus two representatives of Gnetales. Comparisons of sequence dissimilarityindicate that expansion segments (or divergence domains) evolve 6.4 to 10.2times as fast as conserved core regions of 26S rDNA sequences in plants.Additional comparisons indicate that 26S rDNA evolves 1.6 to 2.2 times asfast as and provides 3.3 times as many phylogenetically informativecharacters as 18S rDNA; compared to the chloroplast gene rbcL, 26S rDNAevolves at 0.44 to 1.0 times its rate and provides 2.0 times as manyphylogenetically informative characters. Expansion segment sequencesanalyzed here evolve 1.2 to 3.0 times faster than rbcL, providing 1.5 timesthe number of informative characters. Plant expansion segments have apattern of evolution distinct from that found in animals, exhibiting lesscryptic sequence simplicity, a lower frequency of insertion and deletion,and greater phylogenetic potential.