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Molecular Organization of 5S rDNAs in Rajidae (Chondrichthyes): Structural Features and Evolution of Piscine 5S rRNA Genes and Nontranscribed Intergenic Spacers

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Abstract

The genomic and gene organisation of 5S rDNA clusters have been extensively characterized in bony fish and eukaryotes, providing general issues for understanding the molecular evolution of this multigene DNA family. By contrast, the 5S rDNA features have been rarely investigated in cartilaginous fish (only three species). Here, we provide evidence for a dual 5S rDNA gene system in the Rajidae by sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (NTS) in five Mediterranean species of rays (Rajidae), and in a large number of piscine taxa including lampreys and bony fish. As documented in several bony fish, two functional 5S rDNA types were found here also in the rajid genome: a short one (I) and a long one (II), distinguished by distinct 5S and NTS sequences. That the ancestral piscine genome had these two 5S rDNA loci might be argued from the occurrence of homologous dual gene systems that exist in several fish taxa and from 5S phylogenetic relationships. An extensive analysis of NTS-II sequences of Rajidae and Dasyatidae revealed the occurrence of large simple sequence repeat (SSR) regions that are formed by microsatellite arrays. The localization and organization of SSR within the NTS-II are conserved in Rajiformes since the Upper Cretaceous. The direct correlation between the SSRs extension and the NTS length indicated that they might play a role in the maintenance of the larger 5S rDNA clusters in rays. The phylogenetic analysis indicated that NTS-II is a valuable systematic tool limited to distantly related taxa of Rajiformes.

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Acknowledgments

We greatly appreciated suggestions and criticisms of both anonymous reviewers, which effectively improved the claim and the quality of the manuscript. We also thank T. Labriola and M. Landi for the helpful assistance in editing the manuscript. This work was supported by grants “Canziani” and “Biodiversity” given by the University of Bologna to FT and PP.

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Authors and Affiliations

  1. Molecular Genetics for Environmental and Fishery Resources Laboratory, Interdept. Centre of Research in Environmental Sciences, University of Bologna, Ravenna, Italy

    Paola Pasolini & Fausto Tinti

  2. Stazione Zoologica “Anton Dohrn”, Naples, Italy

    Domenico Costagliola

  3. Department of Life Sciences, Second University of Naples, Caserta, Italy

    Lucia Rocco

  4. Marine Biology and Fishery Laboratory, University of Bologna, Fano, Italy

    Fausto Tinti

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  1. Paola Pasolini
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  2. Domenico Costagliola
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  3. Lucia Rocco
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  4. Fausto Tinti
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Correspondence to Fausto Tinti.

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Pasolini, P., Costagliola, D., Rocco, L. et al. Molecular Organization of 5S rDNAs in Rajidae (Chondrichthyes): Structural Features and Evolution of Piscine 5S rRNA Genes and Nontranscribed Intergenic Spacers. J Mol Evol 62, 564–574 (2006). https://doi.org/10.1007/s00239-005-0118-z

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