Evolutionary trends of As51 satellite DNA and its colocalization with 45S ribosomal DNA: a conserved feature in Characiformes fishes

Satellite DNAs (satDNAs) can arise from diverse genomic regions, but determining their precise origin remains a major challenge. A previous study reported the colocalization of the As51 satDNA and the 45S ribosomal DNA (rDNA) in Astyanax janeiroensis, suggesting a potential evolutionary link between these repetitive elements. However, this observation was based on a single observation and has not been broadly tested. In this study, we investigate whether the association between As51 satDNA and 45S rDNA extends to additional species within Characidae and Characiformes, aiming to uncover broader patterns that may provide insights into the evolutionary origin and dynamics of these genomic components. Using multiple complementary datasets, including raw long-read and short-read sequencing, publicly available genome assemblies, and RNA-seq datasets, alongside customized bioinformatic approaches, we assembled and analyzed 45S rDNA arrays from several Characiformes species. We identified As51-like sequences within the intergenic spacers (IGS) of 45S rDNA across all examined species, with sequence similarity ranging from 45.10% to 90.20%. Notably, the tetra fishes Astyanax mexicanus and Psalidodon paranae exhibited exceptionally high abundance and sequence conservation of As51-like repeats within their rDNA spacers. Fluorescence in situ hybridization (FISH) validated the physical colocalization of As51 satDNA and rDNA clusters in these species. Our findings suggest that the As51 satellite DNA may have originated from the intergenic spacer region of 45S rDNA in an ancestral Characiformes species. The high sequence conservation and abundance observed in tetra fish indicate that this satellite DNA expanded within the spacer regions of certain Acestrorhamphidae and was subsequently dispersed into heterochromatic regions typically occupied by this satellite. This study provides new insights into the evolutionary dynamics of repetitive DNA sequences and offers a model for investigating how satellite DNAs can originate from functional genomic regions and spread across the genome.