# Convergent subgenome dominance but with lineage-specific functional divergence of homoeologs during cave adaptation: insights from full-length transcriptomes of Sinocyclocheilus species

## TL;DR

This study explores how duplicated genomes in cavefish evolved to help them adapt to cave environments, showing that subgenome dominance leads to different adaptations in different species.

## Contribution

The study reveals convergent subgenome dominance and lineage-specific functional divergence in cavefish, linking genome duplication to ecological adaptation.

## Key findings

- Cavefish species show B-subgenome dominance in homoeolog expression, while surface species show balanced expression.
- Subgenome-dominant genes in S. microphthalmus are enriched in immunological elements, indicating immune investment shifts.
- Subgenome-dominant genes in S. furcodorsalis are enriched in neuromodulatory and metabolic pathways, suggesting energy conservation.

## Abstract

Allopolyploidy creates duplicated genomes that drives evolutionary innovation and adaptive diversification under extreme environmental pressures. Although subgenomic architecture is recognized as pivotal in post-polyploid evolution, the mechanisms by which divergent subgenome dynamics shape adaptive potential remain unclear. We investigated how subgenome evolution relates to environmental adaptation in Sinocyclocheilus cavefish, an allotetraploid lineage that repeatedly colonized caves across the karst landscapes of Southwest China. We integrated full-length and short-read transcriptomes from a surface-dwelling species (S. angustiporus) and two independently cave-adapted species (S. microphthalmus and S. furcodorsalis). The two cave dweller species showed consistent B-subgenome dominance in homoeolog expression, whereas the surface species showed balanced expression. Functional enrichment analyses identified lineage-specific functional divergence of dominantly expressed homoeologs. In S. microphthalmus, subgenome-dominant genes were significantly enriched in immunological elements, suggesting an evolutionary shift in immune investment. In S. furcodorsalis, subgenome-dominant genes were significantly enriched in neuromodulatory and metabolic pathways, consistent with energy conservation and sensory regression in nutrient-poor caves. Together, these findings suggest that polyploidy can promote diversification through convergent subgenome dominance. Biased repurposing of distinct stress-responsive modules resolves ancestral genomic conflicts. This, in turn, drives the emergence of lineage-specific functions and links genome duplication to ecological adaptation.

The online version contains supplementary material available at 10.1186/s12983-025-00591-1.