5.8S motifs for the identification of pseudogenic ITS regions

The internal transcribed spacer (ITS) region (ITS 1, 5.8S rDNA, ITS2) represents one of the most popular molecular markers in phylogenetics. The number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenic ITS regions is on the increase. Studies including pseudogenic ITS regions can lead to erroneous phylogenetic trees and false taxonomic conclusions. For their recognition, we focus on the 5.8S rDNA as the functional part of this region, which is also affected by degeneration processes. We outline three conserved Viridiplantae 5.8S motifs: GAATTGCAGAAwyC, TTTGAAyGCA, CGATGAAGAAGyAGC, which can be simply checked in sequence alignments. The latter 5.8S motif we also recognised in the large subunit RNA (LSU) of Escherichia coli. The utility of different methods for pseudogene detection based on easily recognisable 5.8S sequence motifs by comparison with 5.8S secondary structure reconstructions and statistical tests are discussed and illustrated with three previously published angiosperm data sets.