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Abstract Detail


Genetics Section

Harpke, Doerte [1], Peterson, Angela [1].

Identification of 5.8S nrRNA pseudogenes in Mammillaria (Cactaceae).

MOLECULAR studies of 21 species of the large Cactaceae genus Mammillaria representing a variety of intra-generic taxonomic levels have revealed a high degree of intra-generic and intra-individual polymorphism of the 5.8S rDNA. However, intra-individual 5.8S rDNA polymorphism of up to 39 % and up to 7 different types suggests the presence of non-functional nrDNA copies (pseudogenes) in Mammillaria. To identify putative 5.8S rRNA pseudogenes, an extensive analysis of 5.8S rDNA was carried out, including the reconstruction of the proper secondary structure, relative rate tests, bootstrap hypothesis testing, an analysis of methylation-related substitutions and the determination of the GC-content, length variation and comparisons with cDNA sequences. These analyses reveal 58 out of 65 genomic sequences (corresponding to 110 clones) as putative pseudogenes. Pseudogenes are characterised by an accelerated rate of evolution, the inability to build up the proper secondary structure which is often connected with the loss of the conserved 14 bp angiosperm 5.8S motif and a lower GC-content.
According to our investigation, the 5.8S rDNA secondary structure construction together with the relative rate test were the most valuable methods for the detection of pseudogenes. Additionally, conserved angiosperm motifs of ITS1 and ITS2 were compared between genomic and cDNA ITS clones of Mammillaria. Some of these motifs (e.g. ITS1 motif 1, 'TGGT' within ITS2) in combination with the determination of GC-content, length comparisons of the spacers and ITS2 secondary structure (helices II and III) are helpful in the
identification of pseudogene rDNA regions.


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1 - Martin Luther University Halle/Wittenberg, Biozentrum, Weinbergweg 22, Halle (Saale), D-06120, Germany

Keywords:
Mammillaria
pseudogenes
5.8S rDNA
polymorphism
secondary structure
cDNA
Cactaceae.

Presentation Type: Array
Session: 48-79
Location: Auditorium/Bell Memorial Union
Date: Tuesday, August 1st, 2006
Time: 12:30 PM
Abstract ID:121


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