High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: Incomplete concerted evolution and the origin of pseudogenes

Molecular studies of six species from the ancient extant seed plant Cycas, covering a wide range of its morphological diversity and all major areas of distribution, revealed a high level of intra-individual polymorphism of the internal transcribed spacer (ITS1, 5.8S, and ITS2) region, indicative of incomplete nrDNA concerted evolution. Through a range of comparisons of sequence characteristics to functional cDNA ITS copies, including sequence length and substitution variation, GC content, secondary structure stability, the presence of a conserved motif in the 5.8S gene, and evolutionary rates, the PCR amplified divergent genomic DNA ITS paralogs were identified as either putative pseudogenes, recombinants or functional paralogs. This incomplete ITS concerted evolution may be linked to the high number of nucleolar organizer regions in the Cycas genome, and the incomplete lineage sorting due to recent species divergence in the genus. Based on the distribution of a 14 bp deletion, an early evolutionary origin of the pseudogenes is indicated, possibly predating the diversification of Cycas. Due to their early origin combined with the unconstraint evolution of the ITS region in pseudogenes, they accumulate high levels of homoplastic mutations. This leads to random relationships among the pseudogenes due to long-branch attractions, whereas the phylogenetic relationships inferred from the functional ITS paralogs grouped the sequences in species specific clades (except for C. circinalis and C. rumphii). The findings of our extensive study will have a wide significance, for the evolution of these molecular sequences, and their utilization as a major marker for reconstructing phylogenies.