Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that a satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, approximately 140–78 million years ago, while its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satellite DNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within SMRT long reads of Astyanax paranae (536 bp to 3.1 kb) and A. mexicanus (501 bp to 3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satellite DNA evolution.

B or supernumerary chromosomes are dispensable elements that are widely present in numerous eukaryotes. Due to their non-recombining nature, there is an evident tendency for repetitive DNA accumulation in these elements. Thus, satellite DNA plays an important role in the evolution and diversification of B chromosomes and can provide clues regarding their origin. The characiform Prochilodus lineatus was one of the first discovered fish species bearing B chromosomes, with all populations analyzed so far showing one to nine micro-B chromosomes and exhibiting at least three morphological variants (Ba, Bsm, and Bm). To date, a single satellite DNA is known to be located on the B chromosomes of this species, but no information regarding the differentiation of the proposed B-types is available. Here, we characterized the satellitome of P. lineatus and mapped 35 satellite DNAs against the chromosomes of P. lineatus, of which six were equally located on all B-types and this indicates a similar genomic content. In addition, we describe, for the first time, an entire population without B chromosomes.

Complete mitochondrial genomes of the characiform fishes Astyanax fasciatus, Astyanax altiparanae, Hoplias malabaricus (Karyomorph A) and the Gymnotiformes species Gymnotus sylvius and Gymnotus cuia were characterized in the present study. The whole mitogenomes varied from 16,400bp (A. fasciatus) to 17,730 bp (A. altiparanae) long and all of them consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs genes, a control region, and origin of light-strand replication. The gene order was similar among all the analyzed species. The nucleotide content of all mitogenomes was also similar, with 29.58-30.95% for A, 27.02-28.65% for T, 26.29-29.99% for C, and 14.41-15.67% for G.

Crocodilians are one of the oldest extant vertebrate lineages, which exhibits a combination of evolutionary success and morphological resilience that have persisted throughout the history of life on Earth. Such an ability to endure over such a long geological time span is of great evolutionary importance. Here, we performed a comprehensive analysis of the satellite DNA diversity of the extant alligators and caimans, making significant progress in our understanding of the evolution of repetitive regions present in ancient genomes. The alligators and caimans displayed a small number of satDNA families (varying between 3 and 13 satDNAs, in A. sinensis and C. latirostris, respectively) as well as little variation both within and between species, highlighting an exceptional long-term conservation of satDNA elements throughout evolution. We also tracked the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatoridae. Fluorescence in situ experiments showed distinct hybridization patterns for the identical ortholog satDNAs, indicating their inner dynamic evolution. Why, in addition to their previously known low genetic, karyotype, and morphological diversity, have crocodilians altered so little over such a long period of time with such a highly variable genome fraction? We argued that such an "evolutionary package" was likely the outcome of severe demographic declines or founder events and that it represents evolutionary responses to a long-lasting bottleneck history.