Cytogenetic analysis of three species of the genus Haemulon (Teleostei: Haemulinae) from Margarita Island, Venezuela

Cytogenetic characterization, rDNA mapping and quantification of the nuclear DNA content in Seriolella violacea Guichenot, 1848 (Perciformes, Centrolophidae)

Seriolella violacea Guichenot, 1848 is an important component of the fish fauna of the Chilean coast and is of great economic interest. Cytogenetic information for the family Centrolophidae is lacking and the genomic size of five of the twenty-eight species described for this family are is barely known. This study aimed to describe for the first time the karyotype structure via classical and molecular cytogenetics analysis with the goal of identifying the constitutive heterochromatin distribution, chromosome organization of rDNA sequences and quantification of nuclear DNA content. The karyotype of S. violacea is composed of 48 chromosomes, with the presence of conspicuous blocks of heterochromatin on chromosomal pairs one and two. FISH assay with a 5S rDNA probe, revealed the presence of fluorescent markings on the heterochromatic block of pair one. The 18S rDNA sites are located exclusively on pair two, characterizing this pair as the carrier of the NOR. Finally, the genomic size of S. violacea was estimated at 0.59 pg of DNA as C-value. This work represents the first effort to document the karyotype structure and physical organization of the rDNA sequences in the Seriolella genome, contributing with new information to improve our understanding of chromosomal evolution and genomic organization in marine perciforms.

Comparative Cytotaxonomy of Two Species of Fish from the Genus Satanoperca Reveals the Presence of a B Chromosome

The taxonomy of Satanoperca spp. is still unresolved, especially because coloring, one of the main diagnostic characters, is variable among species of this genus. Thus, the aim of this study was to elucidate the relationship between the genome and the organization of the chromosome in two Satanoperca species. Our main goal was to develop a method to better differentiate taxa and understand the evolution of Satanoperca jurupari and Satanoperca lilith karyotypes, which we analyzed with classical and molecular cytogenetics. Both species have the same diploid number (2n) of 48 and location of 5S rDNA sites on pair 5. Nonetheless, the distribution of heterochromatin and 18S rDNA sites followed a species-specific pattern. The interstitial telomeric sites were not highlighted in either species. Regardless, a single B chromosome was identified in some metaphases of S. lilith. These data show that Satanoperca species harbor chromosomal features that can be used to identify the two species of Satanoperca studied here, allowing for the use of cytogenetic markers to make taxonomic inferences within the genus.

Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics

Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

Preferential accumulation of sex and Bs chromosomes in biarmed karyotypes by meiotic drive and rates of chromosomal changes in fishes

Mechanisms of accumulation based on typical centromeric drive or of chromosomes carrying pericentric inversions are adjusted to the general karyotype differentiation in the principal Actinopterygii orders. Here, we show that meiotic drive in fish is also supported by preferential establishment of sex chromosome systems and B chromosomes in orders with predominantly bi-brachial chromosomes. The mosaic of trends acting at an infra-familiar level in fish could be explained as the interaction of the directional process of meiotic drive as background, modulated on a smaller scale by adaptive factors or specific karyotypic properties of each group, as proposed for the orthoselection model.

First description of the karyotype and localization of major and minor ribosomal genes in Rhoadsiaaltipinna Fowler, 1911 (Characiformes, Characidae) from Ecuador

Karyotypic features of Rhoadsiaaltipinna Fowler, 1911 from Ecuador were investigated by examining metaphase chromosomes through Giemsa staining, C-banding, Ag-NOR, and two-color-fluorescence in situ hybridization (FISH) for mapping of 18S and 5S ribosomal genes. The species exhibit a karyotype with 2n = 50, composed of 10 metacentric, 26 submetacentric and 14 subtelocentric elements, with a fundamental number FN=86 and is characterized by the presence of a larger metacentric pair (number 1), which is about 2/3 longer than the average length of the rest of the metacentric series. Sex chromosomes were not observed. Heterochromatin is identifiable on 44 chromosomes, distributed in paracentromeric position near the centromere. The first metacentric pair presents two well-defined heterochromatic blocks in paracentromeric position, near the centromere. Impregnation with silver nitrate showed a single pair of Ag-positive NORs localized at terminal regions of the short arms of the subtelocentric chromosome pair number 12. FISH assay confirmed these localization of NORs and revealed that minor rDNA clusters occur interstitially on the larger metacentric pair number 1. Comparison of results here reported with those available on other Characidae permit to hypothesize that the presence of a very large metacentric pair might represent a unique and derived condition that characterize one of four major lineages molecularly identified in this family.

Chromosome evolution in fishes: a new challenging proposal from Neotropical species

We present a database containing cytogenetic data of Neotropical actinopterygian fishes from Venezuela obtained in a single laboratory for the first time. The results of this study include 103 species belonging to 74 genera assigned to 45 families and 17 out of the 40 teleost orders. In the group of marine fishes, the modal diploid number was 2n=48 represented in 60% of the studied species, while in the freshwater fish group the modal diploid complement was 2n=54, represented in 21.21 % of the studied species. The average number of chromosomes and the mean FN were statistically higher in freshwater fish than in marine fish. The degree of diversification and karyotype variation was also higher in freshwater fish in contrast to a more conserved cytogenetic pattern in marine fish. In contrast to the assumption according to which 48 acrocentric chromosomes was basal chromosome number in fish, data here presented show that there is an obvious trend towards the reduction of the diploid number of chromosomes from values near 2n=60 with high number of biarmed chromosomes in more basal species to 2n=48 acrocentric elements in more derived Actinopterygii.

Evolutionary dynamics of rRNA gene clusters in cichlid fish

Background

Among multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity.

Results

The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes.

Conclusions

The organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a more complete picture for understanding the organization of repeated sequences in the genome.

Genetic characterization of Plectorhinchus mediterraneus yields important clues about genome organization and evolution of multigene families

Background

Molecular and cytogenetic markers are of great use for to fish characterization, identification, phylogenetics and evolution. Multigene families have proven to be good markers for a better understanding of the variability, organization and evolution of fish species. Three different tandemly-repeated gene families (45S rDNA, 5S rDNA and U2 snDNA) have been studied in Plectorhinchus mediterraneus (Teleostei: Haemulidae), at both molecular and cytogenetic level, to elucidate the taxonomy and evolution of these multigene families, as well as for comparative purposes with other species of the family.

Results

Four different types of 5S rDNA were obtained; two of them showed a high homology with that of Raja asterias, and the putative implication of a horizontal transfer event and its consequences for the organization and evolution of the 5S rDNA have been discussed. The other two types do not resemble any other species, but in one of them a putative tRNA-derived SINE was observed for the first time, which could have implications in the evolution of the 5S rDNA. The ITS-1 sequence was more related to a species of another different genus than to that of the same genus, therefore a revision of the Hamulidae family systematic has been proposed. In the analysis of the U2 snDNA, we were able to corroborate that U2 snDNA and U5 snDNA were linked in the same tandem array, and this has interest for tracing evolutionary lines. The karyotype of the species was composed of 2n = 48 acrocentric chromosomes, and each of the three multigene families were located in different chromosome pairs, thus providing three different chromosomal markers.

Conclusions

Novel data can be extracted from the results: a putative event of horizontal transfer, a possible tRNA-derived SINE linked to one of the four 5S rDNA types characterized, and a linkage between U2 and U5 snDNA. In addition, a revision of the taxonomy of the Haemulidae family has been suggested, and three cytogenetic markers have been obtained. Some of these results have not been described before in any other fish species. New clues about the genome organization and evolution of the multigene families are offered in this study.

Characterization of yellow grouper Epinephelus awoara (Serranidae) karyotype by chromosome bandings and fluorescence in situ hybridization

The cytogenetics of yellow grouper Epinephelus awoara was studied using multiple cytogenetic markers [Giemsa staining, C-banding, Ag-NORs and fluorescence in situ hybridization (FISH)]. Giemsa staining results showed that the karyotypic formula of E. awoara was 2n = 48a, FN (fundamental number) = 48. Faint C-bandings were only detected at the centromeric regions of chromosome pair number 24, being almost indiscernible on the other chromosome pairs. After Ag-NOR staining, one pair of nucleolar organizer regions (NOR) was observed in the subcentromeric region of pair number 24. FISH results showed that 5S rDNA was located at a pair of medium-sized chromosomes, while 18S rDNA appeared at the same location in the subcentromeric region of pair number 24 where Ag-NORs were detected. The telomeric sequence (TTAGGG)(n) detected by FISH was located at both ends of each chromosome. The results suggested that E. awoara has retained general karyotypic structure stability during the evolutionary diversification process.

Karyoevolutionary aspects of Atlantic hogfishes (Labridae-Bodianinae), with evidence of an atypical decondensed argentophilic heterochromatin

Fish from the family Labridae elicit considerable ecological interest, especially due to their complex interactions with the reef environment. Different karyoevolutionary tendencies have been identified in the subfamilies Bodianinae, Corinae and Cheilinae. Chromosomal analyses conducted in the Atlantic species Bodianus rufus (2n=48; 6m+12sm+14st+16a, FN=80), Bodianus pulchellus (2n=48; 4m+12sm+14st+18a, FN=78) and Bodianus insularis (2n=48; 4m+12sm+14st+18a, FN=78) identified Ag-NOR/18SrDNA sites located only in the terminal region of the short arm (p) of the largest subtelocentric pair. The 5S rDNA genes were mapped in the terminal region of the long arm (q) of the largest acrocentric pair and the p arm of chromosome 19 in B. insularis. The karyotype of the three species shows an extensive heterochromatic and argentophilic region, exceptionally decondensed, located in the p arm of the second subtelocentric pair. This region does not correspond to a NOR site, since it is not hybridized with 18S rDNA probes, and is not GC-rich, as generally occurs with nucleolus organizer regions of lower invertebrates. Heterochromatin in the three species is reduced and distributed over the centromeric and pericentromeric regions of chromosomes. The elevated number of two-armed chromosomes in species of Bodianus, in relation to other Labridae, shows karyotype diversification based on pericentric inversions, differentiating them markedly in terms of evolutionary tendencies that occur in subfamilies Corinae and Cheilininae. Structural cytogenetic similarities between B. pulchellus and B. insularis, in addition to the conserved chromosomal location pattern of ribosomal multigenic families, indicate phylogenetic proximity of these species.

Chromosome differentiation patterns during cichlid fish evolution

BACKGROUND

Cichlid fishes have been the subject of increasing scientific interest because of their rapid adaptive radiation which has led to an extensive ecological diversity and their enormous importance to tropical and subtropical aquaculture. To increase our understanding of chromosome evolution among cichlid species, karyotypes of one Asian, 22 African, and 30 South American cichlid species were investigated, and chromosomal data of the family was reviewed.

RESULTS

Although there is extensive variation in the karyotypes of cichlid fishes (from 2n = 32 to 2n = 60 chromosomes), the modal chromosome number for South American species was 2n = 48 and the modal number for the African ones was 2n = 44. The only Asian species analyzed, Etroplus maculatus, was observed to have 46 chromosomes. The presence of one or two macro B chromosomes was detected in two African species. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA) gene revealed a variable number of clusters among species varying from two to six.

CONCLUSIONS

The karyotype diversification of cichlids seems to have occurred through several chromosomal rearrangements involving fissions, fusions and inversions. It was possible to identify karyotype markers for the subfamilies Pseudocrenilabrinae (African) and Cichlinae (American). The karyotype analyses did not clarify the phylogenetic relationship among the Cichlinae tribes. On the other hand, the two major groups of Pseudocrenilabrinae (tilapiine and haplochromine) were clearly discriminated based on the characteristics of their karyotypes. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA) gene did not follow the chromosome diversification in the family. The dynamic evolution of the repeated units of rRNA genes generates patterns of chromosomal distribution that do not help follows the phylogenetic relationships among taxa. The presence of B chromosomes in cichlids is of particular interest because they may not be represented in the reference genome sequences currently being obtained.