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. 2018 Oct 26;19(1):97.
doi: 10.1186/s12863-018-0684-x.

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae)

Jenyfer Fernández-Pérez  1 , Ana Nantón  2 , Josefina Méndez  2
Affiliations

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae)

Jenyfer Fernández-Pérez et al. BMC Genet. .

Abstract

Background: The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated.

Results: The length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170-210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies.

Conclusions: This is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources.

Keywords: 5S unit; Donax; Internal transcribed spacer; Ribosomal DNA; Wedge clams.

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Conflict of interest statement

Ethics approval and consent to participate

Compliance with ethical standards. Field work was conducted in accordance with local legislation and with regulations and guidelines established by the University of A Coruña. No endangered or protected species were involved.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Graphical representation of the control elements involved in the transcription of 5S rDNA. The top sequences represent a schematic comparison of the ICRs between Donax consensus sequence and D. melanogaster. The bottom sequences represent a schematic comparison of the sequence elements (box A, intermediate element (IE), and box C) between Donax consensus sequence and X. laevis. The asterisks indicate similarities respect to consensus sequences described for D. melanosgaster and X. laevis
Fig. 2
Fig. 2
Bayesian phylogenetic tree inferred from 5S rDNA sequences of Donax semistriatus, Donax trunculus, Donax variegatus and Donax vittatus. The phylogenetic tree was rooted with Cerastoderma edule and Cerastoderma glaucum species. Numbers at the nodes correspond to Bayesian posterior probabilities
Fig. 3
Fig. 3
Bayesian phylogenetic tree inferred from ITS sequences of Donax semistriatus, Donax trunculus, Donax variegatus and Donax vittatus. The phylogenetic tree was rooted with Cerastoderma edule and Cerastoderma glaucum species. Numbers at the nodes correspond to Bayesian posterior probabilities
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