Paulo Cesar Venere

Chromosome differentiation patterns during cichlid fish evolution.

BackgroundCichlid 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.ResultsAlthough 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.ConclusionsThe 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.

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.

Evolutionary dynamics of rRNA gene clusters in cichlid fish

BackgroundAmong 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.ResultsThe 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.ConclusionsThe 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.

Organization of repeated DNA elements in the genome of the cichlid fish Cichla kelberi and its contributions to the knowledge of fish genomes.

Repeated DNA elements have been extensively applied as physical chromosome markers in comparative studies for the identification of chromosomal rearrangements, the identification of sex chromosomes, chromosome evolution analysis and applied genetics. Here, we report the characterization of the transposable elements (TE) Tc1, Rex1, Rex3 and Rex6 and a new element called RCk in the genome of the South American cichlid fish Cichla kelberi using nucleotide sequence analysis and hybridization to metaphase chromosomes. The analysis of the repeated elements demonstrated that they are, in most cases, compartmentalized in heterochromatic regions, as has been observed in several other vertebrates. On the other hand, the elements Rex1 and Rex3 were also observed spanning extensive euchromatic regions on 2 chromosome pairs. The RCk element exhibits a wide distribution among fishes and also in amphibians, and it was spread throughout the chromosomes of C. kelberi. Our results have demonstrated that the compartmentalization of repeated elements is not restricted to heterochromatic segments, which has provided new concepts with regard to the genomic organization of transposons.

5S rDNA variation and its phylogenetic inference in the genus Leporinus (Characiformes: Anostomidae)

Abstract5S rDNA sequences have proven to be valuable as genetic markers to distinguish closely related species and also in the understanding of the dynamic of repetitive sequences in the genomes. In the aim to contribute to the knowledge of the evolutionary history of Leporinus (Anostomidae) and also to contribute to the understanding of the 5S rDNA sequences organization in the fish genome, analyses of 5S rDNA sequences were conducted in seven species of this genus. The 5S rRNA gene sequence was highly conserved among Leporinus species, whereas NTS exhibit high levels of variations related to insertions, deletions, microrepeats, and base substitutions. The phylogenetic analysis of the 5S rDNA sequences clustered the species into two clades that are in agreement with cytogenetic and morphological data.

A novel ZZ/ZW sex chromosome system for the genus Leporinus (Pisces, Anostomidae, Characiformes)

A wide range of sex chromosome mechanisms, including simple and multiple chromosome systems is characteristic of fishes. The Leporinus genus represent a good model to study sex chromosome mechanisms, because an unambiguous ZZ/ZW sex chromosome system was previously described for seven species, while the remaining studied species of the genus do not show differentiated sex chromosomes. The occurrence of sex chromosomes in Leporinus trifasciatus and Leporinus sp2 from the Araguaia river, Amazon basin, Brazil, was here investigated. ZZ/ZW sex chromosomes were detected for both species. The Z and W chromosome morphology of L. trifasciatus is the same as described for other species of the genus Leporinus. However, the Z and W chromosomes of L. sp2 were quite different in their morphology and banding pattern suggesting that the ZW system of this species have originated independently from the ZW system previously described for other Leporinus.

Comparative cytogenetics in Astyanax (Characiformes: Characidae) with focus on the cytotaxonomy of the group

Astyanax is a diverse group of Neotropical fishes, whose different forms occupy different environments. This great diversity is also reflected on cytogenetic aspects and molecular markers, which have repeatedly been demonstrated by cytogenetic studies. In order to characterize the karyotype of species of this genus, six species were studied: Astyanax altiparanae, A.argyrimarginatus, A. elachylepis, A. xavante, and two new species provisionally called Astyanax sp. and A. aff. bimaculatus. A detailed cytogenetic study based on conventional staining with Giemsa, AgNORs, C-banding, base-specific fluorochromes, and FISH using ribosomal genes 18S and 5S was conducted, aiming to understand some of the chromosomal mechanisms associated with the high diversification that characterizes this group and culminated with the establishment of these species. The results showed 2n = 50 chromosomes for five species and a karyotype with 52 chromosomes in Astyanax sp. Small variations in the macrostructure of the karyotypes were identified, which were quite relevant when analyzed by classical banding, fluorochromes, and FISH methods. These differences among Astyanax spp. (2n = 50) are largely due to changes in the amount and types of heterochromatic blocks. Astyanax sp (2n = 52), in addition to variations due to heterochromatic blocks, has its origin possibly by events of centric fission in a pair of chromosomes followed by minor rearrangements.These results show an interesting karyotypic diversity in Astyanax and indicate the need of a review of the group referred as A. aff. bimaculatus and the description of Astyanax sp., including the possibility of inclusion of this unit in another genus. Astyanax e um grupo bastante diverso de peixes neotropicais cujas diferentes formas ocupam distintos ambientes. Esta grande variabilidade tambem se reflete em aspectos citogeneticos e moleculares, que tem sido repetidamente demonstrados por meio de estudos citogeneticos. A fim de caracterizar o cariotipo de representantes deste genero, seis especies foram estudadas: Astyanax altiparanae, A. elachylepis, A. xavante, A. argyrimarginatus e duas especies novas provisoriamente citadas como Astyanax sp. e A. aff. bimaculatus. Um estudo citogenetico detalhado com base na coloracao convencional com Giemsa, AgNORs, banda C, fluorocromos base-especificos, e FISH com sondas para genes ribossomais 18S e 5S foi realizado com o objetivo de compreender alguns dos mecanismos cromossomicos associados com a alta diversificacao que caracteriza este grupo de peixes e que culminou com o estabelecimento dessas especies. Os resultados revelaram 2n = 50 cromossomos para cinco especies e 2n = 52 cromossomos para Astyanax sp. Pequenas variacoes na macroestrutura dos cariotipos foram identificadas e se mostraram relevantes quando analisadas com base nos bandamentos classicos, coloracao por fluorocromos base-especificos e FISH com sondas de DNA 18S e 5S. Esssa diversidade cariotipica detectada indica a necessidade de uma revisao taxonomica no grupo de individuos aqui referidos como A. aff. bimaculatus, inclusive com a descricao de Astyanax sp., incluindo a possibilidade de insercao dessa unidade em outro genero distinto de Astyanax.

Chromosomal characterization of the bonytongue Arapaima gigas (Osteoglossiformes: Arapaimidae)

The mitotic chromosomes of the pirarucu Arapaima gigas inhabiting the middle Araguaia River and collected in the municipality of Araguaiana (MT, Brazil) were studied. The chromosomes were analyzed through Giemsa staining, C-banding, Ag-NOR staining and in situ hybridization using an 18S rRNA gene probe. The karyotype had 2n=56 comprising 14 biarmed and 14 uniarmed chromosome pairs in both sexes. No cytologically distinguishable sex chromosome was identified. A single NOR-bearing chromosome pair was detected by Ag-NOR staining and confirmed by 18S rDNA- FISH. Faint constitutive heterochromatin was C-banded in the centromeric region of some chromosomes.

Comparative cytogenetics of three populations from the Rhamdia quelen species complex (Siluriformes, Heptapteridae) in two Brazilian hydrographic basins

Abstract Among the more than 30 families of the order Siluriformes, Heptapteridae is composed of 189 species distributed into 24 genera. Rhamdia, which has wide distribution throughout the Neotropical region, presents only 11 valid species, with 8 being in the Brazilian territory. Rhamdia quelen is the only species considered as widely distributed in almost all Brazilian hydrographic basins. It is a Neotropical fish species with a confusing taxonomical history. Classic and molecular cytogenetics data for three populations of this species from two large Brazilian hydrographic basins (Paraná and Araguaia) are presented here. The diploid number found for the three analyzed populations was 58 chromosomes, but with distinct karyotypic formulae. The presence of B chromosomes was detected in the two Araguaia River populations with intra- and interindividual variation. C-banding evidenced little heterochromatin in the three analyzed populations. FISH with 18S rDNA probes evidenced a single chromosome pair bearing this site, confirming the presence of simple NORs, as visualized through silver nitrate staining. The site of 5S rDNA was observed in only one pair of chromosomes, but differing in the marked pair and their location. Based in the differences of the karyotypic formulae and rDNA 5S found between populations on this study and many others available in the literature, it is suggested that this group represents a species complex, and that a new and detailed taxonomical review is necessary.

Comparative cytogenetics of ten species of cichlid fishes (Teleostei, Cichlidae) from the Araguaia River system, Brazil, by conventional cytogenetic methods

Abstract Cichlids represent one of the most species-rich families of fishes and have attracted the attention of evolutionary biologists due to the rapid radiation occurring in some groups and the importance of some species in the world aquaculture. Cytogenetic analysis was conducted in 10 cichlid species from the Araguaia River, Amazon Basin, Brazil. The chromosome number was 2n=48 for all analyzed species except for Laetacara araguaiae Ottoni et Costa, 2009 (2n=44). Chromosomal polymorphism was detected only in Geophagus proximus (Castelnau, 1855), which exhibits an extra large submetacentric and and a dot-like chromosomes. Moreover, the C-banding revealed a general pericentromeric heterochromatic pattern and some additional blocks for some species. The heterochromatic blocks corresponding to AgNOR bearing regions were observed in all species and also corresponded to CMA3 positive blocks, which were observed in terminal regions. Besides the general conserved chromosomal and heterochromatin patterns for South American cichlids, the presence of GC-rich heterochromatin was quite different in the species Biotodoma cupido (Heckel, 1840), Geophagus proximus, Retroculus lapidifer (Castelnau, 1855), Crenicichla strigata Günther, 1862 and Heros efasciatus Heckel, 1840. The results suggest that independent events of heterochromatin modification occurred during chromosome evolution in the group, regardless of the conservation of macro-chromosomal structure.