Retrotransposed DNA sequences in Psalidodon fishes drive genome evolution

Jenn Hoskins
3rd January, 2026

Retrotransposed DNA sequences in Psalidodon fishes drive genome evolution

The proposed evolutionary history from the study suggests the sbno2-B and simc1-B pseudogenes were acquired on a common ancestral B chromosome in the fish genus Psalidodon and maintained through speciation, followed by independent loss in two separate lineages.

Image adapted from: Lasmar et al. / CC BY (Source)

Key Findings

  • Psalidodon fish species carry extra chromosomes, called B chromosomes, which contain fragmented copies of genes from their regular chromosomes
  • These gene fragments, called pseudogenes (sbno2-B and simc1-B), originated from a common ancestor and have been maintained across different Psalidodon species
  • The presence of one B chromosome reduces the expression of the original sbno2 and simc1 genes, potentially helping the B chromosome to be inherited across generations
B chromosomes are extra, ‘supernumerary’ chromosomes found in some species, often behaving differently than regular chromosomes during cell division[2]. While their presence doesn’t always cause obvious harm, they aren’t essential for survival, leading to questions about why they persist across generations. Research from UNESP, Leibniz Institute for Biodiversity Change, University of Bonn, Uppsala University, and Fundacao Oswaldo Cruz[1] investigates the role of these chromosomes in the fish genus Psalidodon, focusing on how they evolve and impact the genome. The study centers on a large B chromosome found in several Psalidodon species. This chromosome contains many repeated DNA sequences and, crucially, fragmented, non-functional copies of genes found on the regular, ‘A’ chromosomes. These copies, called pseudogenes, arise through a process called retrotransposition – effectively, genes making copies of themselves and inserting them elsewhere in the genome. The research team wanted to understand how these pseudogenes evolved and whether they have any functional effects. The researchers focused on two specific genes, sbno2 and simc1, which have been duplicated and fragmented on the B chromosome. They analyzed four different versions of the B chromosome from three Psalidodon species to trace the evolutionary history of the sbno2 and simc1 pseudogenes. They found that the retrotransposition event – the initial copying of these genes onto the B chromosome – likely happened in a common ancestor of these species, before they diverged into separate lineages. After this initial event, the B chromosome evolved differently in each species. In species with a high number of B chromosome copies, the sbno2-B pseudogene was found to exist as dozens of scattered copies, while simc1-B typically had three copies arranged in a row. This difference in copy number suggests different evolutionary pressures acting on these two genes after their insertion onto the B chromosome. Interestingly, when the researchers looked at gene expression in individuals with only one B chromosome (1B), they found reduced levels of sbno2 and simc1 expression in the ovaries. This suggests that the pseudogenes on the B chromosome are interfering with the expression of the functional genes on the A chromosomes. This interference is likely happening through non-coding RNA mechanisms – essentially, the pseudogenes are producing RNA molecules that disrupt the normal regulation of the original genes. This finding aligns with the broader understanding of “selfish genetic elements”[3], where genetic elements prioritize their own transmission, even if it’s detrimental to the organism. B chromosomes are often driven to inherit preferentially, despite potentially causing negative effects. The observed gene expression interference suggests that the B chromosome pseudogenes may be a mechanism for this drive, disrupting the normal genetic balance and ensuring their own propagation. The study builds on earlier research showing that retroposition is a significant source of new genes in mammals[4][5]. While these new genes often evolve new functions, the Psalidodon research highlights another potential outcome: the creation of pseudogenes that influence the expression of existing genes. This can lead to genomic diversity and changes in gene regulatory networks. The findings suggest that retrotransposon activity on B chromosomes isn’t just a random process, but a dynamic force generating genetic variation and potentially contributing to the persistence of these chromosomes in populations.

GeneticsEcologyEvolution

References

Main Study

1) B chromosome retrotransposed sequences persist through speciation, contributing to genomic and regulatory innovations in the fish genus Psalidodon (Characiformes, Acestrorhamphidae)

Published 2nd January, 2026

https://doi.org/10.1371/journal.pone.0340085

Related Studies

2) B Chromosomes - A Matter of Chromosome Drive.

https://doi.org/10.3389/fpls.2017.00210

3) Selfish genetic elements, genetic conflict, and evolutionary innovation.

https://doi.org/10.1073/pnas.1102343108

4) The life history of retrocopies illuminates the evolution of new mammalian genes.

https://doi.org/10.1101/gr.198473.115

5) Burst of young retrogenes and independent retrogene formation in mammals.

https://doi.org/10.1371/journal.pone.0005040


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