Chromosome differentiation patterns during cichlid fish evolution

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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, <it>Etroplus maculatus</it>, 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.</p> <p>Conclusions</p> <p>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.</p

Identificação e caracterização de sequências repetidas de DNA no genoma do ciclídeo Astronotus ocellatus

Uma grande porção do genoma da maioria dos organismos é composta por seqüências repetidas de DNA que foram considerados, por muitos anos, como DNA “egoísta” ou como DNA “lixo”. Pouca atenção tem sido dada a estes segmentos de DNA uma vez que eles não são transcritos em produtos codificantes ou funcionais. Atualmente diversos trabalhos têm sugerido o envolvimento destas seqüências na regulação e reparo de alguns genes, na diferenciação de cromossomos sexuais e na organização estrutural e funcional do genoma. Os estudos citogenético-moleculares, como o mapeamento físico cromossômico, têm demonstrado que as seqüências de DNA repetidas podem ser muito úteis como ferramentas para definir a estrutura e revelar a organização e evolução do genoma das espécies. No presente trabalho, vários elementos repetidos (AoHinfI-4, AoHaeIII-6, AoHaeIII-15) foram isolados, através de restrição enzimática, do genoma do ciclídeo sul-americano Astronotus ocellatus, popularmente conhecido como “Oscar” ou “Apaiari”. Estes elementos foram seqüenciados e utilizados como sondas para hibridação cromossômica para o estudo de seu padrão de distribuição no cariótipo. As seqüências dos elementos repetidos isolados por restrição enzimática apresentaram alta similaridade com outros DNAs repetidos de outras espécies de peixes já depositadas em banco de dados. Os resultados da hibridação in situ de todos os elementos utilizados mostraram um acúmulo de marcações preferencialmente centromérica em todos os cromossomos do complemento. Essas marcações também são coincidentes com a localização da heterocromatina evidenciada através do bandamento C, reforçando a idéia do acúmulo de DNA repetitivo em regiões heterocromáticas. Essa distribuição preferencialmente centromérica dos elementos repetidos isolados sugere que tais seqüências devam desempenhar...In most organisms a great portion of the genome is composed of repetitive DNA sequences. However little attention has been given to these segments of DNA, which were considered by many years as selfish or “junk” DNA. On the other hand, several works have suggested the involvement of these sequences in the regulation and repair of some genes, in the differentiation of sex chromosomes and in the structural and functional organization of the genome. The cytogenetics and molecular studies, as the physical chromosome mapping, has been demonstrating that repetitive sequences can be very useful as tools to define the structure and to reveal the organization and evolution of the genome of the species. In the present work several repetitive elements (retrotransposons Rex1, Rex3 and Rex6; transposon Tc1; the elements AoHinfI-4, AoHaeIII-6, AoHaeIII-15) were isolated using PCR and enzymatic restriction digestion of the genome of the cichlid Astronotus ocellatus, popularly known as Oscar or Apaiari. These elements were sequenced and their genomic distribution determined by chromosomal in situ hybridization. The nucleotide sequences of the isolated elements showed high similarity to repetitive DNAs of other fish species available in public databases. The results of in situ hybridization showed an accumulation of all obtained elements preferentially in centromeres of all chromosomes of the complement. The chromosomal signals were also coincident with the location of the heterocromatins evidenced through the C banding, reinforcing the idea of the accumulation of repetitive DNA in heterocromatic areas. These preferential distribution in the centromeres, suggests that such sequences should play an important role in the functional organizational and structure of the centromeres and, thus in the genome of this species. The great majority of the studies using the physical chromosome mapping... (Complete abstract click electronic access below)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Integrando citogenética e genômica em estudos comparativos entre peixes ciclídeos e outros vertebrados

Os ciclídeos representam um dos exemplos mais marcantes de evolução entre os vertebrados. Por isso, muitos estudos genômicos vêm sendo desenvolvidos para este grupo, incluindo mapas genéticos de ligação, mapas físicos com base em bibliotecas de cromossomos artificiais bacterianos (BAC) e, mais recentemente, o sequenciamento completo de genomas. Bibliotecas de BACs podem ainda ser exploradas no sentido de obtenção de sondas para mapeamento citogenético, fornecendo importantes informações sobre a estrutura e evolução cromossômica das espécies e grupos. Ainda, a análise das sequências nucleotídicas dos BACs em conjunto com mapeamento in silico podem ser utilizadas para integrar dados físicos cromossômicos, sequências gênicas, mapas genéticos e sequências de genomas completos. Esse trabalho teve por objetivo inferir sobre a diversificação cromossômica durante a evolução dos ciclídeos utilizando BACs de bibliotecas genômicas de Oreochromis niloticus para o mapeamento físico citogenético e análises comparativas entre os diversos genomas disponíveis de peixes e outros vertebrados. Os resultados mostram uma forte conservação cromossômica dos marcadores/genes analisados entre as espécies de ciclídeos estudadas. Além disso, análises in silico de citogenética e genômica comparativa mostram grandes segmentos cromossômicos conservados não somente entre os ciclídeos, mas também entre diferentes espécies/grupos de peixes e entre espécies de vertebrados demonstrando evidências de sintenia de grandes segmentos genômicos mesmo entre grupos taxonomicamente distantes em vertebrados. Esses resultados fornecem uma excelente base para futuros estudos de caracterização citogenética e integração de mapas para estudos evolutivos em peixes, em especial na família CichlidaeCichlids represent one of the most striking examples of rapid and convergent evolutionary radiation among vertebrates. Several genomic resources have been developed for cichlid fish, including genetic linkage maps, physical mapping based on bacterial artificial chromosome (BAC) libraries and more recently and whole sequencing genomes. These BACs libraries can be explored to obtain probes for cytogenetic mapping providing important informations about chromosome structure and evolution. Additionally BAC-end sequencing analyzes in combination with in silico mapping can be used to integrate chromosomes, local (gene) sequences, genetic maps, and whole genome sequencing. The present study aimed to infer about the chromosomal diversification during cichlid evolution using BAC clones from Oreochromis niloticus libraries for cytogenetic mapping and a comparative analyzes using fish and other complete genomes available. The results show a strong conservation of number and location of hybridization signals between cichlids species. Furthermore, in silico comparative genomics and cytogenetic analysis showed that large chromosomal segments are conserved not only in cichlids but also among non-related fish groups and either between some vertebrates, providing evidence for large syntenic genomic segments. These results provide an excellent foundation for further cytogenetic characterization and comparative maps for chromosome evolution studies in fishes, especially in the Cichlidae familyCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish

<p>Abstract</p> <p>Background</p> <p>The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alternative means to identify conserved synteny shared by distinct genomes and also to define genome regions that are still not fine characterized even after wide-ranging nucleotide sequence efforts. An efficient way to perform comparative cytogenetic mapping is based on BAC clones mapping by fluorescence <it>in situ</it> hybridization. In this report, to address the knowledge gap on the genome evolution in cichlid fishes, BAC clones of an <it>Oreochromis niloticus</it> library covering the linkage groups (LG) 1, 3, 5, and 7 were mapped onto the chromosomes of 9 African cichlid species. The cytogenetic mapping data were also integrated with BAC-end sequences information of <it>O. niloticus</it> and comparatively analyzed against the genome of other fish species and vertebrates.</p> <p>Results</p> <p>The location of BACs from LG1, 3, 5, and 7 revealed a strong chromosomal conservation among the analyzed cichlid species genomes, which evidenced a synteny of the markers of each LG. Comparative <it>in silico</it> analysis also identified large genomic blocks that were conserved in distantly related fish groups and also in other vertebrates.</p> <p>Conclusions</p> <p>Although it has been suggested that fishes contain plastic genomes with high rates of chromosomal rearrangements and probably low rates of synteny conservation, our results evidence that large syntenic chromosome segments have been maintained conserved during evolution, at least for the considered markers. Additionally, our current cytogenetic mapping efforts integrated with genomic approaches conduct to a new perspective to address important questions involving chromosome evolution in fishes.</p

Comparative cytogenetic mapping of Sox2 and Sox14 in cichlid fishes and inferences on the genomic organization of both genes in vertebrates

To better understand the genomic organization and evolution of Sox genes in vertebrates, we cytogenetically mapped Sox2 and Sox14 genes in cichlid fishes and performed comparative analyses of their orthologs in several vertebrate species. The genomic regions neighboring Sox2 and Sox14 have been conserved during vertebrate diversification. Although cichlids seem to have undergone high rates of genomic rearrangements, Sox2 and Sox14 are linked in the same chromosome in the Etroplinae Etroplus maculatus that represents the sister group of all remaining cichlids. However, these genes are located on different chromosomes in several species of the sister group Pseudocrenilabrinae. Similarly, the ancestral synteny of Sox2 and Sox14 has been maintained in several vertebrates, but this synteny has been broken independently in all major groups as a consequence of karyotype rearrangements that took place during the vertebrate evolution.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq