A tandem array of 5S ribosomal RNA genes in Pythium irregulare

DNA-methylation dependent regulation of embryo-specific 5S ribosomal DNA cluster transcription in adult tissues of sea urchin Paracentrotus lividus

We have previously reported a molecular and cytogenetic characterization of three different 5S rDNA clusters in the sea urchin Paracentrotus lividus and recently, demonstrated the presence of high heterogeneity in functional 5S rRNA. In this paper, we show some important distinctive data on 5S rRNA transcription for this organism. Using single strand conformation polymorphism (SSCP) analysis, we demonstrate the existence of two classes of 5S rRNA, one which is embryo-specific and encoded by the smallest (700 bp) cluster and the other which is expressed at every stage and encoded by longer clusters (900 and 950 bp). We also demonstrate that the embryo-specific class of 5S rRNA is expressed in oocytes and embryonic stages and is silenced in adult tissue and that this phenomenon appears to be due exclusively to DNA methylation, as indicated by sensitivity to 5-azacytidine, unlike Xenopus where this mechanism is necessary but not sufficient to maintain the silenced status.

5S rDNA gene diversity in tea (Camellia sinensis (L.) O. Kuntze) and its use for variety identification

Variability in the organization of repeats of 5S rDNA is useful for phylogenetic studies in various crops. We found variable repeats of 5S rDNA gene in the genome of tea (Camellia sinensis (L.) O. Kuntze) during Southern hybridization. Variability in the repeats of 5S rDNA with specific restriction endonuleases (Sau3AI, BamHI, and ApoI) was analyzed in 28 different tea clones representing 3 types of tea. Our results clearly show that the 5S rDNA gene in tea could be used as a molecular marker to distinguish C. sinensis Chinary tea from the other important types of tea, namely Assamica and Cambod. Upon analysis with restriction endonucleases, the 5S rDNA gene in the tea genome was found to be heavily methylated.Key words: Camellia sinensis, 5S rDNA, DNA methylation, restriction endonucleases, molecular marker.

Diversity and evolution of 5S rRNA gene family organization in Pythium

The 5S rRNA gene family organization among 87 species and varieties of Pythium was investigated to assess evolutionary stability of the two patterns detected and to determine which pattern is likely the ancestral state in the genus. Species with filamentous sporangia (Groups A-C according to the ITS phylogenetic tree for Pythium) had 5S genes linked to the rDNA repeat that were predominantly coded for on the DNA strand opposite to the one with the other rRNA genes ('inverted' orientation). A small group of species with contiguous sporangia (Group D) is related to Groups A-C but had unlinked 5S genes. The main group of species with spherical zoosporangia (Groups E-J) generally had unlinked 5S genes in tandem arrays. The six species in Group K, although they also have spherical sporangia, had linked genes on the same strand as the other rRNA genes 'non-inverted' and most of them had pairs of tandem 5S genes. The evolutionary stability of 5S sequence organization was compared with the stability of morphological characters as interpreted from a phylogeny based on ITS sequence analysis. Features of 5S sequence organization were found to be just as consistent within groups as were the morphological characters. To determine the ancestral type of 5S family organization, a survey of Phytophthora strains was conducted to supply an outgroup reference. The most parsimonious interpretation of the data in this survey yielded the tentative conclusion that the linked condition of the 5S sequences was ancestral.

Discrimination of three trachurus species using both mitochondrial- and nuclear-based DNA approaches

A double-DNA approach was developed to discriminate the three Trachurus species that abide in European waters: T. trachurus, T. mediterraneus, and T. picturatus. The analysis aimed at both mitochondrial and nuclear loci. Polymerase Chain Reaction (PCR) amplification of the cytochrome b gene of mtDNA was followed by restriction analysis with three species-specific enzymes: NlaIII, NciI, and BsmAI. Digestion with these endonucleases yielded species-specific electrophoretic profiles. The universality of the results was verified by screening a large number of individuals from 12 geographical regions covering most of the distribution of the species. Additionally, the nuclear multicopy 5S rRNA gene was selected as an alternative candidate for the discrimination of the three Trachurusspecies. A simple agarose gel electrophoretic analysis of the amplicons proved to be capable of leading to unambiguous identification of the three Trachurus species. Thus, the double-DNA methodology presented here allows the accurate discrimination of Trachurus fish species and the detection of commercial fraud.

Identification of goose (Anser anser) and mule duck (Anasplatyrhynchos x Cairina moschata) foie gras by multiplex polymerase chain reaction amplification of the 5S RDNA gene

Polymerase chain reaction (PCR) amplification of the nuclear 5S rDNA gene has been used for the identification of goose and mule duck foie gras. Two species-specific reverse primers were designed and used in a multiplex reaction, together with a forward universal primer, to amplify specific fragments of the 5S rDNA in each species. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear identification of goose and mule duck foie gras samples. This genetic marker can be useful for detecting fraudulent substitution of the duck liver for the more expensive goose liver.

Identification of sole (Solea solea) and Greenland halibut (Reinhardtius hippoglossoides) by PCR amplification of the 5S rDNA gene

Polymerase chain reaction (PCR) amplification of the nuclear 5S rDNA gene, has been used for the identification of sole (Solea solea) and Greenland halibut (Reinhardtius hippoglossoides). Two species-specific primers were designed to amplify specific fragments of the 5S rDNA gene in each species. The remarkably different size of the amplicons obtained gives, by simple agarose gel electrophoresis, two distinguishable band patterns for both flatfish species. This genetic marker can be very useful for the accurate identification of S. solea and Greenland halibut, to enforce labeling regulations.