Emergence of satellite DNAs suggests centromeric repositioning as a driver of karyotypic variation of the freshwater darter characines (Apareiodon affinis)

TL;DR

This study explores how satellite DNA sequences contribute to chromosomal variation in a species of freshwater fish, suggesting centromeric repositioning as a key mechanism.

Contribution

The study identifies specific satellite DNA sequences involved in centromeric repositioning and chromosomal diversification in Apareiodon affinis.

Findings

Intragenomic homogenization and intergenomic mechanisms diversify satellite DNA sequences in A. affinis.

The satellite AafSat01-200 is uniquely localized to centromeres of acrocentric chromosomes and is the most abundant in the genome.

Centromeric repositioning is linked to the expansion of acrocentric chromosomes in this species.

Abstract

Repetitive DNA sequences actively contribute to karyotype diversification by accumulating mutations, exhibiting susceptibility to DNA double-strand breaks that promote chromosomal rearrangements, and reshuffling within centromeric heterochromatin, among other processes. Parodontidae shows a conserved diploid number of 54, with predominantly metacentric and submetacentric chromosomes. Apareiodon affinis, from the Lower Paraná River, was described with three karyomorphs due to interpopulation structural variation, characterized by four to sixteen acrocentric chromosomes. However, the mechanisms driving chromosomal variation and the contribution of satellite DNA to these processes remain poorly understood. In this study, we characterized the A. affinis satellitome to assess the role of satellite sequences in the diversification of acrocentric chromosomes. A total of 48 satellite DNAs were identified, and 16 of them were mapped in situ. The data demonstrated that intragenomic homogenization mechanisms led to alterations in satellite sequence dominance, and intergenomic mechanisms contributed to the diversification of orthologous sequences when compared with other Characiformes families. In situ localization revealed that most satellites in the centromeric regions of acrocentric chromosomes were absent from the centromeres of meta/submetacentric chromosomes. The satellite AafSat01-200, which is highly diversified and the most abundant in the A. affinis genome, exhibits exclusive centromere localization on acrocentric chromosomes. Our results indicate the presence of distinct monomers with centromeric function in A. affinis and identify AafSat01-200 as the principal element involved in the centromeric repositioning mechanism that led the expansion of acrocentric chromosomes in this lineage.

The online version contains supplementary material available at 10.1007/s10577-026-09793-7.

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