Synchronised developmental partitioning of visual opsins across parental subgenomes in allopolyploid Barbus barbus

Abstract

Hybridisation and whole-genome duplication generate evolutionary novelty by combining and duplicating divergent parental genomes. Yet, how organisms differentially deploy duplicated gene repertoires across development remains poorly understood. The vertebrate visual system provides an excellent model for addressing this question because colour vision depends on the tightly regulated expression of opsin genes, which often undergo pronounced ontogenetic changes. Here, using comparative transcriptomics, we show that the allopolyploid common barbel (Barbus barbus) has evolved coordinated developmental partitioning of duplicated cone opsin genes. During ontogeny, the short-wavelength-sensitive opsins SWS1 and SWS2 switch expression between parental-subgenome ohnologs, while the middle-wavelength-sensitive RH2 switches between tandem paralogs, with all three transitions being synchronised. In contrast, the long-wavelength-sensitive LWS ohnologs from both parental genomes remain co-expressed throughout development. Single-nucleus RNA sequencing further revealed a strongly rod-dominated retina and largely conserved expression of phototransduction genes across recent ohnologs. The retention of all 14 visual opsin genes and their differential developmental deployment in common barbel highlights the value of independently evolved allopolyploid lineages for investigating the evolutionary consequences of genome duplication. More broadly, our findings show how hybridisation and genome duplication can enable divergent expression of parental gene copies, potentially contributing to sensory adaptation over evolutionary timescales.