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.Résumé : La région (ITS) de l'espaceur interne transcrite (ITS1, 5.8S rADN, ITS2) représente un des marqueurs des plus populaires en phylogénie. On observe une augmentation du nombre de recherches montrant une présence importante accrue de polymorphisme intra individuel, reliée avec la présence de régions ITS pseudogènes. Les études incluant des ré-gions ITS pseudogènes peuvent conduire à des arbres phylogénétiques erronés et à de fausses conclusions taxonomiques. Afin de les reconnaître, les auteurs se concentrent sur le 5.8S rADN comme partie fonctionnelle de cette région, laquelle est également affectée par le processus de dégénérescence. Ils soulignent trois motifs 5.8S Viridiplantae : GAATTGCAGAAwyC, TTTGAAyGCA, CGATGAAGAACGyAGC, qu'on peut simplement vérifier en alignements de séquences. Ils reconnaissent également le dernier motif 5.8S dans la grande sous-unité ARN (LSU) chez l'Escheria coli. On discute l'utilité de différentes méthodes pour détecter les pseudogènes, basées sur des motifs de séquences facilement reconnaissables du 5.8S, comparativement aux reconstructions secondaires et aux tests statistiques; trois ensembles de données provenant d'angiospermes et préalablement publiées, servent à illustrer ce propos.
The taxonomically complicated Crocus series Verni is characterized by high intra-and interspecific variability of karyotypes (2n = 8-23). With the aim to get more insights into complex karyotype evolution and to clarify the taxonomy of this group, we combined morphological (twelve characters), molecular (chloroplast DNA: trnL-trnF, ndhF; nuclear DNA: ITS, pCOSAt103) and karyological analyses. Samples of different populations of C. etruscus, C. ilvensis, C. kosaninii, C. tommasinianus, C. vernus sensu lato and C. longiflorus (series Longiflori) were analyzed. Quantitative karyotype parameters were calculated for all taxa involved based on the available literature. For the taxon traditionally known as C. vernus, the analyses suggest that it should be split in five species: C. heuffelianus, C. neapolitanus, C. neglectus sp. nov., C. siculus and C. vernus. The comparison of genome total haploid lengths suggests that in the evolution of the group polyploidization only played a role within the C. vernus species complex, where we also detected two hybridization events. In all other taxa, chromosome evolution is probably characterized by chromosome fusions and fissions, sometimes affecting the entire haploid chromosome set. Comparative cytogenetics of the group indicates that series Verni is subject to a peculiar type of unequal change in chromosome size, i.e., that not both chromosome arms gain or lose equally in DNA content. As a taxonomic consequence of our study, series Verni is newly circumscribed, now including the autumn-flowering C. longiflorus and excluding C. baytopiorum.
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