Supernumerary chromosome system, C-banding pattern characterization and multiple nucleolus organizer regions in Moenkhausia sanctaefilomenae (Pisces, Characidae)

Occurrence of euchromatic B chromosomes in natural populations of Moenkhausia bonita and M. forestii (Pisces: Characidae)

ABSTRACT Moenkhausia is a highly specious genus among the Characidae, composed of 96 valid species. Only twelve species have a known karyotype. Thus, here are presented the first cytogenetic data of two allopatric populations of Moenkhausia bonita and one of M. forestii, both belonging to the upper Paraná River basin (PR) with discussion on the evolutionary and cytotaxonomic aspects of the genus. The two species presented 2n = 50 chromosomes but different karyotype formulas and occurrence of 1-2 B chromosomes. These elements are small metacentrics in M. bonita and small acrocentrics in M. forestii. In both species, B chromosomes were euchromatic. Ag-NOR sites were found in pair 3 (metacentric), coinciding with fluorescent in situ hybridization (FISH) by the 18S rDNA probe in both species. However, the species differed in terms of the number and position of 5S rDNA sites. Heterochromatic blocks, mapped in M. bonita showed the least amount of heterochromatin in the terminal and pericentromeric regions, while the M. forestii karyotype revealed a greater amount of interstitial heterochromatic blocks. The karyotype distinctions between the two species, including the morphology of B chromosomes, may contribute as a reference in the taxonomic studies in this group.

Molecular cytogenetic analyses reveal extensive chromosomal rearrangements and novel B chromosomes in Moenkhausia (Teleostei, Characidae)

The cytogenetic characteristics of five fish species of the Moenkhausia are described, based on the analysis of specimens collected in different headwater. All the species analyzed presented 2n=50 chromosomes. The C-banding revealed a similar distribution pattern of heterochromatic blocks in all the species, except Moenkhausia nigromarginata. The 5S rDNA sites were distributed on multiple chromosome pairs in all five species. Single and multiple histone H1 sites were observed in all the species, and histone H1 was shown to be co-located with the 18S rRNA gene in a single chromosome pair. The U2 snDNA gene was distributed at multiple sites in all the Moenkhausia species. The presence of B microchromosomes was confirmed in Moenkhausia forestii, while individuals of the three study populations of Moenkhausia oligolepis presented three morphologically distinct types of B chromosome. The chromosomal mapping of the 18S rDNA sites using the FISH technique revealed signals in the B chromosomes of M. forestii, while clusters of the H1 histone and U2 snDNA genes were found in the B chromosomes of M. forestii and M. oligolepis. The classical and molecular cytogenetic markers used in this study revealed ample variation in the Moenkhausia karyotypes, reflecting the dynamic nature of the chromosomal evolution.

Uncovering the Ancestry of B Chromosomes in Moenkhausia sanctaefilomenae (Teleostei, Characidae)

B chromosomes constitute a heterogeneous mixture of genomic parasites that are sometimes derived intraspecifically from the standard genome of the host species, but result from interspecific hybridization in other cases. The mode of origin determines the DNA content, with the B chromosomes showing high similarity with the A genome in the first case, but presenting higher similarity with a different species in the second. The characid fish Moenkhausia sanctaefilomenae harbours highly invasive B chromosomes, which are present in all populations analyzed to date in the Parana and Tietê rivers. To investigate the origin of these B chromosomes, we analyzed two natural populations: one carrying B chromosomes and the other lacking them, using a combination of molecular cytogenetic techniques, nucleotide sequence analysis and high-throughput sequencing (Illumina HiSeq2000). Our results showed that i) B chromosomes have not yet reached the Paranapanema River basin; ii) B chromosomes are mitotically unstable; iii) there are two types of B chromosomes, the most frequent of which is lightly C-banded (similar to euchromatin in A chromosomes) (B₁), while the other is darkly C-banded (heterochromatin-like) (B₂); iv) the two B types contain the same tandem repeat DNA sequences (18S ribosomal DNA, H3 histone genes, MS3 and MS7 satellite DNA), with a higher content of 18S rDNA in the heterochromatic variant; v) all of these repetitive DNAs are present together only in the paracentromeric region of autosome pair no. 6, suggesting that the B chromosomes are derived from this A chromosome; vi) the two B chromosome variants show MS3 sequences that are highly divergent from each other and from the 0B genome, although the B₂-derived sequences exhibit higher similarity with the 0B genome (this suggests an independent origin of the two B variants, with the less frequent, B₂ type presumably being younger); and vii) the dN/dS ratio for the H3.2 histone gene is almost 4–6 times higher for B chromosomes than for A chromosome sequences, suggesting that purifying selection is relaxed for the DNA sequences located on the B chromosomes, presumably because they are mostly inactive.

Whole chromosome painting of B chromosomes of the red-eye tetra Moenkhausia sanctaefilomenae (Teleostei, Characidae)

B chromosomes are dispensable genomic elements found in different groups of animals and plants. In the present study, a whole chromosome probe was generated from a specific heterochromatic B chromosome occurring in cells of the characidae fish Moenkhausia sanctaefilomenae (Steindachner, 1907). The chromosome painting probes were used in fluorescence in situ hybridization (FISH) experiments for the assessment of metaphase chromosomes obtained from individuals from three populations of Moenkhausia sanctaefilomenae. The results revealed that DNA sequences were shared between a specific B chromosome and many chromosomes of the A complement in all populations analyzed, suggesting a possible intra-specific origin of these B chromosomes. However, no hybridization signals were observed in other B chromosomes found in the same individuals, implying a possible independent origin of B chromosome variants in this species. FISH experiments using 18S rDNA probes revealed the presence of non-active ribosomal genes in some B chromosomes and in some chromosomes of the A complement, suggesting that at least two types of B chromosomes had an independent origin. The role of heterochromatic segments and ribosomal sequences in the origin of B chromosomes were discussed.

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.

Single origin of sex chromosomes and multiple origins of B chromosomes in fish genus Characidium

Chromosome painting with DNA probes obtained from supernumerary (B) and sex chromosomes in three species of fish genus Characidium (C. gomesi, C. pterostictum and C. oiticicai) showed a close resemblance in repetitive DNA content between B and sex chromosomes in C. gomesi and C. pterostictum. This suggests an intraspecific origin for B chromosomes in these two species, probably deriving from sex chromosomes. In C. oiticicai, however, a DNA probe obtained from its B chromosome hybridized with the B but not with the A chromosomes, suggesting that the B chromosome in this species could have arisen interspecifically, although this hypothesis needs further investigation. A molecular phylogenetic analysis performed on nine Characidium species, with two mtDNA genes, showed that the presence of heteromorphic sex chromosomes in these species is a derived condition, and that their origin could have been unique, a conclusion also supported by interspecific chromosome painting with a CgW probe derived from the W chromosome in C. gomesi. Summing up, our results indicate that whereas heteromorphic sex chromosomes in the genus Characidium appear to have had a common and unique origin, B chromosomes may have had independent origins in different species. Our results also show that molecular phylogenetic analysis is an excellent complement for cytogenetic studies by unveiling the direction of evolutionary chromosome changes.

Comparative cytogenetics among populations of Hollandichthys multifasciatus (Teleostei: Characidae)

Two populations of Hollandichthys multifasciatus from headwaters of adjacent river coastal basins in Paraná state, southern Brazil, were cytogenetically studied in order to evaluate intraspecific divergences. Both populations presented 2n = 50 chromosomes, divided into 14m + 18sm + 18st in the sample from Antonina and 14m + 20sm + 16st for the population from Guaraqueçaba. Analyses of active nucleolar organizer regions (Ag-NORs) and fluorescent in situ hybridization (FISH) with 18S rDNA probes revealed a single metacentric pair bearing marks at proximal positions on the short arms. The location of the 5S rDNA and GC-rich sites showed chromosomal divergence between both populations. Therefore, several population markers were detected, reflecting a population differentiation, possibly driven by the formation of Paranaguá Bay and Serra do Mar mountain range. Since the existence of a species complex in H. multifasciatus has been previously characterized by morphological, molecular, and karyotype population differentiation, this species needs to be taxonomically studied in detail.

Genomic content and new insights on the origin of the B chromosome of the cichlid fish Astatotilapia latifasciata

B chromosomes are additional chromosomes widely studied in a diversity of eukaryotic groups, including fungi, plants and animals, but their origin, evolution and possible functions are not clearly understood. To further understand the genomic content and the evolutionary history of B chromosomes, classical and molecular cytogenetic analyses were conducted in the cichlid fish Astatotilapia latifasciata, which harbor 1–2 B chromosomes. Through cytogenetic mapping of several probes, including transposable elements, rRNA genes, a repeated DNA genomic fraction (C0t - 1 DNA), whole genome probes (comparative genomic hybridization), and BAC clones from Oreochromis niloticus, we found similarities between the B chromosome and the 1st chromosome pair and chromosomes harboring rRNA genes. Based on the cytogenetic mapping data, we suggest the B chromosome may have evolved from a small chromosomal fragment followed by the invasion of the proto-B chromosome by several repeated DNA families.

Cytogenetic analysis of B chromosomes in one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907) (Teleostei, Characiformes)

The aim of this study was to characterize cytogenetically one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907), with emphasis on the analysis of B chromosomes. The nucleolar activity in the B microchromosomes was characterized, and an analysis of mitotic instability of these microchromosomes was accomplished. The results showed a diploid chromosome number of 50 chromosomes. In all individuals, we observed the presence of B microchromosomes with intra- and inter-individual variability. The analysis of the nucleolus organizing regions (NORs) by silver nitrate staining demonstrated multiple NORs. We observed active sites of ribosomal DNA in the B microchromosomes, with a frequency of 20% in the analyzed cells, which shows gene activity in these chromosomal elements. The analysis of constitutive heterochromatin patterns showed that the B microchromosomes are heterochromatic or euchromatic, which demonstrates differentiation of DNA composition between these genomic elements. The calculation of the mitotic instability index implied that B chromosomes in this species might be in a final stage of instability.

Flow cytometric determination of genome size in European sunbleak Leucaspius delineatus (Heckel, 1843)

The aim of this study was to compare DNA content in hepatocyte and erythrocyte nuclei of the European sunbleak, Leucaspius delineatus, in relation to nuclear and cell size by means of flow cytometry and fluorescence microscopy. The DNA standards, chicken and rainbow trout erythrocytes, were prepared in parallel with both cell types, with initial separation of liver cells in pepsin solution followed by cell filtering. Standards and investigated cells were stained with a mixture of propidium iodide, citric acid, and Nonidet P40 in the presence of RNAse, and fluorescence of at least 50,000 nuclei was analyzed by flow cytometry. Average cell size was determined by flow cytometry, using fresh cell suspension in relation to latex beads of known diameter. The size of nuclei was examined on the basis of digital micrographs obtained by fluorescence microscopy after nuclei staining with DAPI. The sunbleak's erythrocyte nuclei contain 2.25 ± 0.06 pg of DNA, whereas the hepatocyte nuclei contain 2.46 ± 0.06 pg of DNA. This difference in DNA content was determined spectroscopically using isolated DNA from the two cell types. The modal diameters of the erythrocytes and hepatocytes were estimated to be 5.1 ± 0.2 and 22.3 ± 5.0 μm, respectively, and the corresponding modal dimensions of their nuclei (measured as surface area) were 15.2 and 21.4 μm(2), respectively. The nucleoplasmic index, as calculated from diameters estimated from surface area of nuclear profiles, was 2.51 for the erythrocytes compared with 0.08 for hepatocytes.

First record of supernumerary (B) chromosomes in electric fish (Gymnotiformes) and the karyotype structure of three species of the same order from the upper Paraná River basin

Cytogenetic studies were performed on the species Apteronotus prope albifrons Linnaeus, 1766, Rhamphichthys hahni Meinken, 1937 and Brachyhypopomus gauderio Giora & Malabarba, 2009, collected in the upper Paraná River floodplain, Porto Rico (PR), Brazil. Apteronotus prope albifrons showed a diploid number of 2n=24 chromosomes for both sexes and a karyotype formula of 14m+2sm+2st+6a (FN=42). Besides the standard karyotype, three specimens had one to three extra microchromosomes with inter- and intra-individual variations, which suggested the occurrence of B chromosomes in the species. The chromosomal data of Rhamphichthys hahni, described here for the first time, consists of 50 chromosomes and a formula comprised of 20m+24sm+6a (FN=94). Brachyhypopomus gauderio specimens demonstrated 2n=42 chromosomes infemales, all acrocentric, and 2n=41 chromosomes in males, with 40 acrocentric and 1 medium-sized metacentric chromosome. These differences concern with a multiple system of sexchromosome determination X1X1X2X2/X1X2Y (FN=42) in Brachyhypopomus gauderio. The analysis of nucleolar organizer regions by Ag-NOR and FISH 18S banding revealed a simple NOR system in Apteronotus prope albifrons and Rhamphichthys hahni and a multiple NOR system in Brachyhypopomus gauderio, that is unusual for Gymnotiformes fishes. Constitutive heterochromatin was mainly found in the pericentromere region in most of the chromosomes of the three species, although each species had its own peculiarities. The B chromosomes in Apteronotus prope albifrons demonstrated heterochromatin positioned in the centromeric and telomeric regions whereas Rhamphichthys hahni presented conspicuous blocks of heterochromatin on the long arms in three submetacentric pairs. Brachyhypopomus gauderio showed blocks of heterochromatin on the long arm in the interstitial and telomere positions. The finding of B chromosomes in Apteronotus prope albifrons represents the first description of these elements in the Gymnotiformes order. Although the karyotype of this species is similar with that described for populations in the Amazon basin, the presence of B chromosomes could represent a specific characteristic of this population. A comparative analysis of karyotypes of Rhamphichthys hahni with other species of the genus showed a relatively conservative structure suggesting 2n=50 as a common number in this group. The karyotype of Brachyhypopomus gauderio, a new species, provides an important reference for future chromosome studies of the Brachyhypopmus Mago-Lecia, 1994, and it might be also significant for cytotaxonomy in this group. The cytogenetic data also demonstrate the need of more comparative cytogenetic studies in the families of the highly diversified and taxonomically difficult complex Gymnotiformes.

The B chromosomes of the African cichlid fish Haplochromis obliquidens harbour 18S rRNA gene copies

BACKGROUND

Diverse plant and animal species have B chromosomes, also known as accessory, extra or supernumerary chromosomes. Despite being widely distributed among different taxa, the genomic nature and genetic behavior of B chromosomes are still poorly understood.

RESULTS

In this study we describe the occurrence of B chromosomes in the African cichlid fish Haplochromis obliquidens. One or two large B chromosome(s) occurring in 39.6% of the analyzed individuals (both male and female) were identified. To better characterize the karyotype and assess the nature of the B chromosomes, fluorescence in situ hybridization (FISH) was performed using probes for telomeric DNA repeats, 18S and 5S rRNA genes, SATA centromeric satellites, and bacterial artificial chromosomes (BACs) enriched in repeated DNA sequences. The B chromosomes are enriched in repeated DNAs, especially non-active 18S rRNA gene-like sequences.

CONCLUSION

Our results suggest that the B chromosome could have originated from rDNA bearing subtelo/acrocentric A chromosomes through formation of an isochromosome, or by accumulation of repeated DNAs and rRNA gene-like sequences in a small proto-B chromosome derived from the A complement.

Phylogeny of the family Characidae (Teleostei: Characiformes): from characters to taxonomy

The family Characidae is the most diverse among Neotropical fishes. Systematics of this family are mainly based on pre-cladistic papers, and only recently a phylogenetic hypothesis for Characidae was proposed by the author. That phylogeny was based on 360 morphological characters studied for 160 species, including representatives of families related to Characidae. This paper is based on that phylogenetic analysis, with the analyzed characters described herein and documented, accompanied by comparisons of their definition and coding in previous papers. Synapomorphies of each node of the proposed phylogeny are listed, comparisons with previous classifications provided, and autapomorphies of the analyzed species listed. Taxonomic implications of the proposed classification and the position of the incertae sedis genera within Characidae are discussed. A discussion of the phylogenetic information of the characters used in the classical systematics of the Characidae is provided.

Genetics of neotropical fish: from chromosomes to populations

The Neotropical freshwater fish fauna is very rich--according to the most recent catalogue 71 families and 4,475 species have been described. However, only a small amount of general information is available on the composition of Neotropical marine fishes. In Brazil, 1,298 marine species have been recorded. General analysis of available cytogenetic and population genetic data clearly indicates research has been mainly concentrated on freshwater fishes. Thus, today, cytogenetic information is available for 475 species of Characiformes, 318 species of Siluriformes, 48 species of Gymnotiformes, 199 freshwater species that do not belong to the superorder Ostariophysi, and only 109 species of marine fishes. For the species studied, only about 6% have sex chromosomes and about 5% have supernumerary or B chromosomes. A review of the cytogenetic studies shows that these data have provided valuable information about the relationships between fish groups, the occurrence of cryptic species and species complexes, the mechanism of sex determination and sex chromosome evolution, the distribution of nucleolus organizer regions, the existence supernumerary chromosomes, and the relationship between polyploidy and evolution. In relation to populations in Neotropical marine waters, the studies have shown the presence of cryptic species, which has important implications for fishery management. Different levels of genetic structuring can be found among Neotropical freshwater migratory fish species. This raises important implications for fish population genetic diversity and consequently its sustainable utilization in inland fisheries and aquaculture, specifically for conservation of ichthyo-diversity and survival.

Cytogenetics of the bleak (Alburnus alburnus), with special emphasis on the B chromosomes

Some of the largest B chromosomes so far discovered in vertebrates are present in the cyprinid fish Alburnus alburnus. Previous cytogenetic analyses revealed a diploid chromosome number of 2n = 50. In addition, in some individuals one or two unusually large B chromosomes are present. Two morphologically different types of B chromosomes were observed. The frequency of animals bearing a supernumerary chromosome was found to vary considerably between different populations. A more detailed analysis of the A and B chromosomes of A. alburnus by conventional banding techniques, as well as fluorescence in-situ hybridization (FISH) with the telomeric DNA repeats (GGGTTA)7/(TAACCC)7, 18S + 28S rDNA and 5S rDNA were performed in the present study. Furthermore, a B chromosome-specific DNA probe obtained by amplified length polymorphism (AFLP) was hybridized on metaphases of A. alburnus carrying supernumerary B chromosomes. The banding analyses showed that the B chromosomes are completely heterochromatic, consist of GC-rich DNA sequences, replicate their DNA in the very late S-phase of the cell cycle and are composed mainly of a specific retrotransposable DNA element. Finally, blood probes from A. alburnus were collected for DNA-flow cytometric measurements. It could be shown that the huge supernumerary chromosomes represent nearly 10% of the total genome size of A. alburnus.

Multiple Nors in Bryconamericus aff. exodon (Osteichthyes, Characidae, Tetragonopterinae)

Fifteen examples of Bryconamericus aff. exodon from the Três Bocas stream in the basin of the Tibagi river (Parana, Brazil) were analyzed. They presented a diploid number of 52 chromosomes. Multiple NORS were detected by silver nitrate impregnation in the telomeric region on the short or long arm of different chromosomes, showing a variation from 2 to 5 NOR-bearing chromosomes. Treatment with chromomycin A3 (CMA3) showed regions rich in GC in different chromosomes, probably coincident with the AgNORS. In situ hybridization by fluorescence (FISH) with 18S rDNA probe showed 8 hybridization signs in the telomeric regions of the chromosomes, proving that this B. aff. exodon population has a greater number of ribosomal cistrons than were detected by Ag-banding.

New cases of supernumerary chromosomes in characiform fishes

Supernumerary chromosomes were described for five species of Neotropical characiform fishes. These extra chromosomes were small, acrocentric and fully heterochromatic in Leporinus friderici from two different localities as well as in Leporinus sp., but metacentric and fully heterochromatic in Cyphocharax modesta and Prochilodus nigricans. In Characidium cf. zebra, this element was small, acrocentric and euchromatic. GC-rich DNA blocks were observed in the supernumerary chromosome of Leporinus sp. using chromomycin A3. The widespread occurrence of these extra chromosomal elements suggests their independent origins.