The chromosomal characterization of the mussels of the family Mytilidae includes the knowledge of mitotic chromosome numbers and karyotypes in 32 species. Six of these species show the same diploid chromosome number (2n = 32) present in both Brachidontes puniceus and B. rodriguezi . On the contrary, the only other species of this genus in which the karyotype has been described, B. pharaonis, shows 2n = 28 chromosomes . The variability of chromosome numbers between species of the same genus is widespread in the family Mytilidae; with the exception of Mytilus, all genera of mussels in which karyotypes have been determined for more than one species show differences in chromosome numbers . On the other hand, the coincidence in chromosome numbers in B. puniceus and B. rodriguezi is accompanied by considerable differences in karyotype composition.
The detection of the vertebrate telomeric (TTAGGG)n repeat at chromosome ends in Brachidontes puniceus and B. rodriguezi agrees with results obtained in chromosomes of other species of bivalves , including the mussels Mytilus galloprovincialis [6, 28] and Perumytilus purpuratus . On the contrary, the interstitial telomeric sequences clearly detected by FISH in P. purpuratus  and presumably appearing in M. galloprovincialis  were not detected in these two species of Brachidontes. Although in bivalves telomeric sequences have only been isolated and characterized in Donax trunculus , the hybridization results obtained so far indicate that the bivalve telomeres are composed of tandem repeats of the hexanucleotide which also constitutes the vertebrate telomeric sequence.
The presence of major rDNA signals on CMA bright regions terminally located on a single chromosome pair in Brachidontes puniceus and on two chromosome pairs in B. rodriguezi is concordant with results obtained in other bivalves. NORs have been located in around 50 species of bivalves [2, 5] and are located at terminal positions on one to three chromosome pairs. In the family Mytilidae, the position of major rRNA genes is known in seven species. One NOR-bearing chromosome pair has been detected in B. pharaonis , two in Mytilus galloprovincialis , M. edulis , B. rodriguezi  and Perumytilus purpuratus , and three in M. trossulus and M. californianus . The species of the genus Brachidontes show differences both in number and chromosomal location of the NORs. The single major ribosomal gene cluster appears at a terminal position on the long arm of one small subtelocentric chromosome pair in both B. puniceus and B. pharaonis . However, the two major ribosomal gene clusters of B. rodriguezi are spread over the whole short arms of the two subtelocentric/telocentric chromosomes pairs .
The occurrence of individuals showing a different number of rDNA clusters to those usually found in the species has been described in many taxa, including humans . In this sense, the presence of an additional NOR in one of the B. puniceus specimens is not remarkable and could be the result of a translocation process as proposed for human ectopic NORs . The absence of one of the major rDNA clusters in one chromosome in B. rodriguezi can be attributed to unequal crossover events .
The mostly coincident FISH signal sizes obtained at the terminal NORs after using 28S rDNA and telomeric probes in both B. rodriguezi and B. puniceus might indicate that some telomeric repeats are interspersed within the major rDNA repeats; fiber-FISH and molecular analysis are necessary to confirm or discard this hypothesis. Although not common, interspersion of telomeric and major ribosomal DNA sequences has been observed in bivalves, such as the mussel Mytilus galloprovincialis  and the scallop Patinopecten yessoensis , and in other organisms such as fishes  and mammals . The meaning of such organization is not well understood but a functional role in nucleolus organization for tandem repeats has been proposed .
The chromosomal location of 5S rDNA clusters is only known in 15 species of bivalves [2, 5]. In most of these species, minor rDNAs usually appear at interstitial loci [18–20]. The presence of two 5S rDNA clusters in both Brachidontes puniceus and B. rodriguezi differs from the results obtained in Mytilus edulis and M. galloprovincialis , in which four 5S rDNA clusters appear on three chromosome pairs, and Perumytilus purpuratus , showing three 5S rDNA clusters on two chromosome pairs. Regarding the other species of bivalves in which the location of these sequences is known, the Ostreidae [13, 14] and two species of Pectinidae [15, 17] also show two 5S rDNA clusters. On the contrary, Cerastoderma edule (Cardiidae) presents five clusters of 5S rDNA on five different chromosome pairs  and most species of Pectinidae show a single 5S rDNA cluster [16, 18, 20].
The variation in number of 5S rDNA FISH signals detected in Brachidontes rodriguezi is mostly due to the presence or absence of signals in chromosome pair # 3. The small size of these signals probably indicates that the number of 5S rDNA repeats at this locus is close to the minimum necessary for the signal to be detected. Similar variations in the number of 5S rDNA signals have been detected in two other species of Mytilidae, Mytilus galloprovincialis and M. edulis .
Our results demonstrate that major and minor rDNA clusters are on different chromosome pairs in Brachidontes puniceus but that in B. rodriguezi one of the NOR-bearing chromosome pairs also carries one of the 5S rDNA clusters. This is also the case in Perumytilus purpuratus  and Chlamys farreri  but differs from the presence of both major and 5S rDNA clusters on different chromosome pairs in the rest of the bivalve species studied so far.
Histone genes are usually organized as tandem repeats in invertebrate genomes . These clusters can be composed by a copy of each one of the core histone genes or both core and linker histone genes. Histone gene arrangement in bivalves has been studied in the mussels Mytilus edulis [21, 23] and M. galloprovincialis [22, 24], and the scallop Chlamys farreri . All of them present clusters of core histone genes ordered in the same way thus probably indicating a conserved arrangement. Our results showing hybridization signals at the same positions after FISH using H3 gene and H2B/H2A gene probes point also to this situation in Brachidontes puniceus and B. rodriguezi. Histone genes are known to be located in two chromosome pairs in the mussel M. galloprovincialis  and the scallop Patinopecten yessoensis  but forming a single cluster in other mussel species, Perumytilus purpuratus , and in the scallops Argopecten irradians, Chlamys farreri and C. nobilis . Therefore, in the family Mytilidae, the presence of two histone gene clusters in these two Brachidontes species coincides with the situation in M. galloprovincialis  but differs from the one in P. purpuratus .
One of the histone gene clusters and one of the 5S rDNA clusters appear on the long arm of the same chromosome pair in both Brachidontes puniceus and B. rodriguezi. In addition, the relative positions of these clusters with respect to the centromere are similar in both species being the histone genes distal to the 5S rDNA. Although these facts seem to indicate that this chromosome is conserved, further analyses are necessary in order to determine their homology. The only other species of bivalves in which the position of these two sequences was investigated together is Perumytilus purpuratus . In contrast with B. puniceus and B. rodriguezi, in P. purpuratus the single histone gene cluster and the 5S rDNA clusters are located in different chromosome pairs.
The similarities in the chromosomal distribution of major rDNA, 5S rDNA and core histone gene clusters found in Brachidontes puniceus, B. rodriguezi and Perumytilus purpuratus  are not shared by Mytilus galloprovincialis [11, 22, 24] and confirm the closeness of P. purpuratus to the species of Brachidontes, therefore keeping open the possibility of its assignation to this genus but discarding that P. purpuratus, B. rodriguezi and B. darwinianus belongs to the same taxon .