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Berlin Brandenburg


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  • 1
    In: Botany (Botanique), 2008, Vol.86(3), pp.300-305
    Description: 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.
    Description: La rgion (ITS) de lespaceur interne transcrite (ITS1, 5.8S rADN, ITS2) reprsente un des marqueurs des plus populaires en phylognie. On observe une augmentation du nombre de recherches montrant une prsence importante accrue de polymorphisme intra individuel, relie avec la prsence de rgions ITS pseudognes. Les tudes incluant des rgions ITS pseudognes peuvent conduire des arbres phylogntiques errons et de fausses conclusions taxonomiques. Afin de les reconnatre, les auteurs se concentrent sur le 5.8S rADN comme partie fonctionnelle de cette rgion, laquelle est galement affecte par le processus de dgnrescence. Ils soulignent trois motifs 5.8S Viridiplantae: GAATTGCAGAAwyC, TTTGAAyGCA, CGATGAAGAACGyAGC, quon peut simplement vrifier en alignements de squences. Ils reconnaissent galement le dernier motif 5.8S dans la grande sous-unit ARN (LSU) chez l Escheria coli . On discute lutilit de diffrentes mthodes pour dtecter les pseudognes, bases sur des motifs de squences facilement reconnaissables du 5.8S, comparativement aux reconstructions secondaires et aux tests statistiques trois ensembles de donnes provenant dangiospermes et pralablement publies, servent illustrer ce propos.
    Keywords: 5.8s Rdna ; Motif ; Pseudogene ; Internal Transcribed Spacer Region ; 5.8 Radn ; Motif ; Pseudogne ; Rgion De Lespaceur Interne Transcrite
    ISSN: 1916-2790
    E-ISSN: 1916-2804
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