ITS2 variants as molecular fossils in plant genomes

Molecular fossils can be useful for reconstructing the evolution of species. However, the molecular fossils preserved in all extant plant genomes are currently absent. In this study, we used barcoded pyrosequencing and phylogenetic analysis to characterize intra-genomic variants of the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA across 178 plant species. We discovered that 97.8% of the species possessed fewer than 4 dominant ITS2 patterns in plant genomes and some patterns in 43.8% of the species can be considered molecular fossils. Further, we demonstrated how these multiple-copy sequences can offer insights into patterns of genetic divergence and phylogenetic history at the species and genus levels. This analysis provides additional information for those studies where single-copy gene has been insufficient. Our results may remarkably contribute to knowledge relating to DNA barcoding and yield crucial clues about the molecular evolution of the plant kingdom.