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

## TL;DR

This study explores how B chromosomes in Psalidodon fish retain and evolve retrotransposed gene copies, influencing gene regulation and contributing to genomic diversity.

## Contribution

The study reveals that B chromosomes in Psalidodon fish retain and diversify retrotransposed pseudogenes, impacting gene regulation and genomic innovation.

## Key findings

- Retrotransposition of sbno2 and simc1 genes occurred in an ancestral B chromosome, with distinct evolutionary trajectories in different species.
- High-copy B chromosomes show multiple sbno2-B and simc1-B pseudogene copies, suggesting structural diversity.
- Underexpression of sbno2 and simc1 in ovaries of Psalidodon paranae suggests B chromosome pseudogenes influence gene regulation via non-coding RNA.

## Abstract

B chromosomes are supernumerary genetic elements rich in repetitive DNA. Many species within the fish genus Psalidodon possess a large metacentric B chromosome that exhibits signs of recent retrotransposon activity, resulting in truncated pseudogenic copies of standard A chromosomes genes, specifically sbno2 and simc1. We aimed to characterize the structure of the B chromosome pseudogenes sbno2-B and simc1-B and their evolutionary history in four B chromosome variants of three Psalidodon species, as well as their expression patterns in Psalidodon paranae individuals with a single B chromosome (1B). Our findings suggest that the retrotransposition process of each gene occurred in an ancestral B chromosome, which later diverged into distinct trajectories within each species following speciation. In the high-copy B chromosomes, the sbno2-B pseudogene shows dozens of interspersed copies, while the simc1-B pseudogene usually shows three copies arranged in tandem. In Psalidodon paranae 1B individuals, underexpression of the sbno2 and simc1 genes in ovaries indicates that the pseudogenic B copies probably influence gene expression through non-coding RNA interference mechanisms. This shows that the retrotransposon activity on B chromosomes generates genomic diversity and neofunctionalization, impacting gene regulatory networks, and possibly contributing to the persistence of B chromosome in populations.