Chromosome number and karyotype of Donax trunculus L. (Mollusca, Bivalvia, Tellinacea)

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

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.

Electronic supplementary material

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

Are Pericentric Inversions Reorganizing Wedge Shell Genomes?

Wedge shells belonging to the Donacidae family are the dominant bivalves in exposed beaches in almost all areas of the world. Typically, two or more sympatric species of wedge shells differentially occupy intertidal, sublittoral, and offshore coastal waters in any given locality. A molecular cytogenetic analysis of two sympatric and closely related wedge shell species, Donax trunculus and Donax vittatus, was performed. Results showed that the karyotypes of these two species were both strikingly different and closely alike; whilst metacentric and submetacentric chromosome pairs were the main components of the karyotype of D. trunculus, 10–11 of the 19 chromosome pairs were telocentric in D. vittatus, most likely as a result of different pericentric inversions. GC-rich heterochromatic bands were present in both species. Furthermore, they showed coincidental 45S ribosomal RNA (rRNA), 5S rRNA and H3 histone gene clusters at conserved chromosomal locations, although D. trunculus had an additional 45S rDNA cluster. Intraspecific pericentric inversions were also detected in both D. trunculus and D. vittatus. The close genetic similarity of these two species together with the high degree of conservation of the 45S rRNA, 5S rRNA and H3 histone gene clusters, and GC-rich heterochromatic bands indicate that pericentric inversions contribute to the karyotype divergence in wedge shells.

Telomeric localization of the vertebrate-type hexamer repeat, (TTAGGG)n, in the wedgeshell clam Donax trunculus and other marine invertebrate genomes

The hexamer repeat sequence (TTAGGG)(n), found at the ends of all vertebrate chromosomes, was previously identified as the main building element of one member of a HindIII satellite DNA family characterized in the genome of the bivalve mollusc Donax trunculus. It was also found in 22 perfect tandem repeats in a cloned junction region juxtaposed to the proper satellite sequence, from which the DNA tract encompassing the clustered tandem copies was excised and subcloned. Here, the chromosomal distribution of (TTAGGG)(n) sequences in the Donax was studied by the sensitivity to Bal31 exonuclease digestion, fluorescence in situ hybridization (FISH) on metaphase chromosomes and rotating-field gel electrophoresis. To verify the occurrence of the hexamer repeat in the genomes of taxonomically related molluscs and other marine invertebrates, genomic DNA from the mussel Mytilus galloprovincialis and the echinoderm Holothuria tubulosa was also analyzed. The kinetics of Bal31 hydrolysis of high molecular mass DNA from the three marine invertebrates revealed a marked decrease over time of the hybridization with the cloned (TTAGGG)(22) sequence, concomitantly with a progressive shortening of the positively reacting DNA fragments. This revealed a marked susceptibility to exonuclease consistent with terminal positioning on the respective chromosomal DNAs. In full agreement, FISH results with the (TTAGGG)(22) probe showed that the repeat appears located in telomeric regions in all chromosomes of both bivalve molluscs. The presence of (TTAGGG)(n) repeat tracts in marine invertebrate telomeres points to its wider distribution among eukaryotic organisms and suggests an ancestry older than originally presumed from its vertebrate distinctiveness.

DNA content, karyotypes, and chromosomal location of 18S-5.8S-28S ribosomal loci in some species of bivalve molluscs from the Pacific Canadian coast

The DNA content of 10 species of bivalve molluscs from British Columbia coast was determined by image analysis, and the karyotypes of the horse clam Tressus capax, the bent-nose macoma Macoma nasuta, and the nuttall's mahogany clam Nuttallia nuttallii are described here for the first time. We also have analyzed the location of rDNA loci using a 28S-5.8S-18S probe in four of these species: Mytilus californianus, M. trossulus, Macoma nasuta and N. nuttallii. Results obtained report new data about cytogenetic characteristics of bivalve molluscs.