Journal of Plant Research

, Volume 121, Issue 3, pp 261–270

Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions

Authors

  • Doerte Harpke
    • BiozentrumMartin Luther University of Halle-Wittenberg
    • BiozentrumMartin Luther University of Halle-Wittenberg
Regular Paper

DOI: 10.1007/s10265-008-0156-x

Cite this article as:
Harpke, D. & Peterson, A. J Plant Res (2008) 121: 261. doi:10.1007/s10265-008-0156-x

Abstract

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

Keywords

5.8S rDNAIntra-individual variabilityMammillariaPseudogeneSecondary structure

Supplementary material

10265_2008_156_MOESM1_ESM.pdf (22 kb)
ESM (PDF 21 kb)

Copyright information

© The Botanical Society of Japan and Springer 2008