The internal transcribed spacer (ITS) region (ITS1, 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, CGATGAAGAACGyAGC, 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.

Crocus sativus, the saffron crocus, is the source of saffron, which is made from the dried stigmas of the plant. It is a male-sterile triploid lineage that ever since its origin has been propagated vegetatively. Its mode of evolution and area of origin are matters of long-lasting debates. Here we analyzed chloroplast genomes and genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) to infer the parent and area of origin of C. sativus. These data were complemented by genome size measurements and analyses of nuclear single-copy genes. We could place 99.3% of saffron GBS alleles in Crocus cartwrightianus, a species occurring in southeastern mainland Greece and on Aegean islands, identifying it as the sole progenitor of the saffron crocus. Phylogenetic and population assignment analyses together with chloroplast polymorphisms indicated the C. cartwrightianus population in the vicinity of Athens as most similar to C. sativus. We conclude that the crop is an autotriploid that evolved in Attica by combining two different genotypes of C. cartwrightianus. Triploid sterility and vegetative propagation prevented afterwards segregation of the favorable traits of saffron, resulting in worldwide cultivation of a unique clonal lineage.