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

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.

A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

“…spp., Erythroculter ilishaeformis Bleeker, Populus fremontii S. Watson, etc. [ 36 , 42 , 43 , 44 ]. In the studied Elaeagnaceae species, there was one TATA-like motif in the NTSs of Sh.…”

“…[ 34 , 36 ]. TATATA, TGATATA, and TATTTA occur in the NTSs of different Donax species, TTATAT in Engistomops spp., TTATGTA in H. rhamnoides and most of the other variants [ 25 , 42 , 43 ]. Assessing the functionality of these modified TATA-boxes as regulatory elements (TATA-box is a signal sequence for RNA polymerase II/III [ 45 ]) is difficult, and a lot of in vitro translation experiments are required.…”

Identificación molecular del Toxocara canis en caninos del cantón Salcedo, Ecuador

“…Siendo de mayor importancia, al considerar los criterios de Huang et al (2017), quienes demuestran que las herramientas moleculares como la PCR convencional resultan de gran importancia en el diagnóstico de especies parasitarias como los nematodos, debido a su elevada especificidad y sensibilidad [18], muy útiles en casos donde las similitudes entre los huevos y los estados larvarios de los helmintos entorpecen la identificación entre especies. El presente estudio confirmó que la secuencia de la región del espaciador transcrito interno (ITS-2) del ADN ribosómico (383 pb) de T. canis, es una región muy conservada (Figura 2), tal como había sido planteado en otros estudios donde se describe que la región ITS contiene dos regiones no codificadoras variables que se encuentran dentro de las repeticiones altamente conservadas del ADNr, entre la subunidad pequeña, la región para 5.8S y los genes para ADNr de la subunidad grande [19]. Estudios basados en el ADN para identificar las especies de nematodos, particularmente utilizando fragmentos de la región ITS del ADN ribosomal demuestran la eficacia de las técnicas moleculares en estudios epidemiológicos [20].…”

The Development of New Species-Specific Molecular Markers Based on 5S rDNA in Elaeagnus L. Species

“…Moreover, 5S rRNA genes are organized as tandemly repeated DNA with monomers that consist of a conservative 120 bp coding part and a variable non-coding part (NTS) [18,19]. It was revealed that NTSs often show species-specific polymorphisms [20,21]. The authors successfully used such polymorphisms to develop species-specific molecular markers in a range of plants [22][23][24][25].…”