Repetitive DNA sequences, including tandem and dispersed repeats, comprise a large portion of eukaryotic genomes and are important for gene regulation, sex chromosome differentiation, and karyotype evolution. In Parodontidae, only the repetitive DNAs WAp and pPh2004 and rDNAs were previously studied using fluorescence in situ hybridization. This study aimed to build a library of repetitive DNA in Parodontidae. We isolated 40 clones using C o t-1; 17 of these clones exhibited similarity to repetitive DNA sequences, including satellites, minisatellites, microsatellites, and class I and class II transposable elements (TEs), from Danio rerio and other organisms. The physical mapping of the clones to chromosomes revealed the presence of a satellite DNA, a Helitron element, and degenerate short interspersed element (SINE), long interspersed element (LINE), and tc1-mariner elements on the sex chromosomes. Some clones exhibited dispersed signals; other sequences were not detected. The 5S rDNA was detected on an autosomal pair. These elements likely function in the molecular degeneration of the W chromosome in Parodontidae. Thus, the location of these elements on the chromosomes is important for understanding the function of these repetitive DNAs and for integrative studies with genome sequencing. The presented data demonstrate that an intensive invasion of TEs occurred during W sex chromosome differentiation in the Parodontidae.

Background B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their biology is still enigmatic. Recent advances in omics and big data technologies are revolutionizing the B biology field. These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. Several genes have been detected on the B chromosomes, although the interaction of B sequences and the normal genome remains poorly understood. Results We identified 727 miRNA precursors in the A. latifasciata genome, 66% which were novel predicted sequences that had not been identified before. We were able to report the A. latifasciata-specific miRNAs and common miRNAs identified in other fish species. For the samples carrying the B chromosome (B+), we identified 104 differentially expressed (DE) miRNAs that are down or upregulated compared to samples without B chromosome (B−) (p < 0.05). These miRNAs share common targets in the brain, muscle and gonads. These targets were used to construct a protein-protein-miRNA network showing the high interaction between the targets of differentially expressed miRNAs in the B+ chromosome samples. Among the DE-miRNA targets there are protein-coding genes reported for the B chromosome that are present in the protein-protein-miRNA network. Additionally, Gene Ontology (GO) terms related to nuclear matrix organization and response to stimulus are exclusive to DE miRNA targets of B+ samples. Conclusions This study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. We observed that the B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes.

The karyotypes of three armored catfish species (Loricariidae) from the Iguaçu river, southern of the Brazil, were compared using different techniques: C-banding, Ag-NOR and fluorescence in situ hybridization (FISH), which used 5S and 18S rDNAs and total Cot-1 fraction as probes. Hypostomus commersoni and Hypostomus derbyi presented 2n = 68 chromosomes, with karyotype formulae 12m+12sm+14st+30a and 12m+12sm+10st+34a, respectively; whereas Hypostomus myersi presented 2n = 74 chromosomes and 12m+16sm+12st+34a. The chromosomal localization of the Ag-NORs, 5S and 18S rDNAs differed in number of sites and chromosomal localization among the studied species. The total Cot-1 probe permitted the visualization of the repetitive DNA fraction in karyotypes of each species. Crosshybridizations using total Cot-1 probe revealed that these species have repetitive DNAs in common. However, this does not occur in H. commersoni in relation to the other species. The apparent karyotype similarity suggests a close relationship between the sympatric H. commersoni and H. derbyi species, but the small differences detected in the examined chromosomal markers indicate evolutionary divergence due to gene flow restriction among them. Hence, the present findings indicate different composition of repetitive sequences among studied species, which permit to infer its role in chromosomal differentiation of Hypostomus.

No abstract

Todos os eucariotos (protozoários, fungos, plantas e animais) têm genomas constituídos por cromossomos lineares com uma porção chamada de telômero em suas extremidades. Os telômeros possuem diversas funções, dentre elas proteger a integridade dos cromossomos ao evitar que as extremidades se unam umas às outras; também estão associados ao processo de envelhecimento, pois ao longo da vida do indivíduo os telômeros vão se encurtando e diminuindo a capacidade das células se dividirem e, por isso, muita gente imagina que seria ótimo se os cientistas desenvolvessem um remédio para que nossos telômeros nunca mais se encurtassem e pudéssemos, assim, adiar o envelhecimento. Mas será mesmo que apenas os telômeros são responsáveis pelo processo de envelhecimento? Qual a importância deles para a saúde da célula? O que aconteceria se pudéssemos ter telômeros longos, sem perda de tamanho, por toda a vida? Seríamos imortais?

Background B chromosomes are extra elements found in several eukaryote species. Usually, they do not express a phenotype in the host. However, advances in bioinformatics over the last decades have allowed us to describe several genes and molecular functions related to B chromosomes. These advances enable investigations of the relationship between the B chromosome and the host to understand how this element has been preserved in genomes. However, considering that transposable elements (TEs) are highly abundant in this supernumerary chromosome, there is a lack of knowledge concerning the dynamics of TE control in B-carrying cells. Thus, the present study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of TEs in gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. Results Through small RNA-seq and genome assembly, we predicted and annotated piRNA clusters in the A. latifasciata genome for the first time. We observed that these clusters had biased expression related to sex and the presence of the B chromosome. Furthermore, three piRNA clusters, named curupira, were identified in the B chromosome. Two of them were expressed exclusively in gonads of samples with the B chromosome. The composition of these curupira sequences was derived from LTR, LINE, and DNA elements, representing old and recent transposition events in the A. latifasciata genome and the B chromosome. The presence of the B chromosome also affected the expression of piRNA pathway genes. The mitochondrial cardiolipin hydrolase-like (pld6) gene is present in the B chromosome, as previously reported, and an increase in its expression was detected in gonads with the B chromosome. Conclusions Due to the high abundance of TEs in the B chromosome, it was possible to investigate the origin of piRNA from these jumping genes. We hypothesize that the B chromosome has evolved its own genomic guardians to prevent uncontrolled TE mobilization. Furthermore, we also detected an expression bias in the presence of the B chromosome over A. latifasciata piRNA clusters and pathway genes.

OOs cromossomos supernumerários B são encontrados em uma variedade de organismos eucariotos e não seguem os padrões de segregação da herança mendeliana. No ciclídeo Astatotilapia latifasciata esse cromossomo está presente em ambos os sexos. No entanto, pouco se sabe sobre a função e comportamento desse elemento. Este trabalho teve como objetivo compreender a relação entre transcritos de mRNA e miRNA em gônadas de A. latifasciata, que possam estar ligadas ao fator sexo e presença do cromossomo B. Para construção do micRNoma de gônadas B+ e B- foram utilizadas bibliotecas de sequenciamento next-generation Illumina – HiSeq do Laboratório Genômica Integrativa (UNESP). As bibliotecas foram submetidas ao processo de filtro pelo software FASTX Toolkit 0.0.13. A identificação e análise de expressão dos microRNAs com base no genoma de A. latifasciata foi realizada através do programa miARma v1.5. Com a finalidade de prospectar 3’UTR dos possíveis targets submeteu-se o genoma e transcriptoma de A. latifasciata ao treinamento de máquina utilizando Augustus v3.1.0. A predição de interação 3’UTR:miRNA foi realizada por 3 softwares. Os melhores resultados foram selecionados (energia livre menor que -16 kcal/mol para miRanda v3.3a e FindTar3, e context-score maior que -0,2 para TargetScan 6.0), totalizando 2.048 predições. Como filtro para a seleção das interações relacionadas ao cromossomo B e sexo foi prospectado os targets que interagiram com miRNAs diferencialmente expressos em ambos os sexos B+ e B- (pvalue =< 0,05 e FDR =< 0,05). O resultado final mostrou uma lista que engloba 18 interações reportadas no banco de dados do TargetScanFish 6.2 envolvendo 9 genes e 5 miRNAs diferencialmente expressos. Além de funções relacionadas a ciclo celular e replicação do DNA (genes alvos fbxo33 e anxa11) foram encontrados nessa lista final genes envolvidos com organização e motilidade de microtúbulos (dnah5 e reep1). A interação dnah5:miR-460 ocorreu em fêmeas e machos B+. MiR-214 esteve diferencialmente expresso em fêmeas B+ e reportou como alvo o gene reep1. Os resultados contribuem para a investigação funcional do cromossomo B, pois, há processos celulares diferencialmente regulados em indivíduos B+, que estão sob controle de miRNAs.