A Glimpse into the Satellite DNA Library in Characidae Fish (Teleostei, Characiformes)

Abstract

Satellite DNA (satDNA) is an abundant fraction of repetitive DNA in eukaryotic genomes and plays an important role in genome organization and evolution. In general, satDNA sequences follow a concerted evolutionary pattern through the intragenomic homogenization of different repeat units. In addition, the satDNA library hypothesis predicts that related species share a series of satDNA variants descended from a common ancestor species, with differential amplification of different satDNA variants. The finding of a same satDNA family in species belonging to different genera within Characidae fish provided the opportunity to test both concerted evolution and library hypotheses. For this purpose, we analyzed here sequence variation and abundance of this satDNA family in ten species, by a combination of next generation sequencing (NGS), PCR and Sanger sequencing, and fluorescence in situ hybridization (FISH). We found extensive between-species variation for the number and size of pericentromeric FISH signals. At genomic level, the analysis of 1000s of DNA sequences obtained by Illumina sequencing and PCR amplification allowed defining 150 haplotypes which were linked in a common minimum spanning tree, where different patterns of concerted evolution were apparent. This also provided a glimpse into the satDNA library of this group of species. In consistency with the library hypothesis, different variants for this satDNA showed high differences in abundance between species, from highly abundant to simply relictual variants.

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

“…Human chromosome centromeres are populated by α satDNA (αSAT) organized in HORs that are structurally distinct and confer chromosome specificity [39,42]. Complex HORs have been found in non-human mammals such as insects, mouse, swine, bovids, horse, dog and elephant (reviewed in [43]), and more recently in Callitrichini monkeys [44] and Teleostei fish [45]. SatDNA arrays are mainly found clustered in heterochromatin, although studies also report the presence of short satDNA arrays dispersed along euchromatic regions [2][3][4][5][6][7].…”

“…This number has been surpassed by a recent study where 164 satDNA families have been identified in Teleostei fish, being this the biggest satellitome characterized for a given species so far [70]. The availability of a methodology capable of assessing satDNA array abundance and diversity led to an explosion of comparative studies across a wide range of clades, including mammals, insects and plants (e.g., [44,45,69,[71][72][73]) providing insights into these sequences.…”

The Tritryps comparative repeatome: insights on repetitive element evolution in Trypanosomatid pathogens

“…RepeatExplorer was originally conceived to analyze plant repeatomes, it has been successfully applied in mammals (Pagán et al 2012), insects (Ruiz-Ruano et al 2016Palacios-Gimenez et al 2017;Pita et al 2017) and fishes (Utsunomia et al 2017). Here, we used low-coverage sequencing and the RepeatExplorer approach to compare the repeatomes of T. cruzi, L. major and T. brucei seeking for insights into the evolution of repetitive sequences in these pathogenic parasites.…”

Are Pericentric Inversions Reorganizing Wedge Shell Genomes?

“…A similar situation was expected in the two wedge shell species, that is, differentially amplified satellite DNAs as the major constituents of these heterochromatic GC-rich bands. Further work including next-generation sequencing, satellite DNA searching, and FISH-mapping [ 52 , 53 , 54 ] will be needed to confirm this.…”