Cell Type Resolved Expression of Duplicate Genes Retained From Whole Genome Duplication in Atlantic salmon

The functional and evolutionary outcomes of whole genome duplication (WGD) events are driven by global remodeling of gene expression. Most investigations of gene expression changes following WGD have applied bulk transcriptomics using tissue samples, thus failing to resolve affected cell types. Here, we leverage single-cell transcriptomics of liver tissue in Atlantic salmon (Salmo salar L.) to quantify cell-specific expression and transcriptional responses to a bacterial infection with Aeromonas salmonicida for thousands of duplicate gene pairs (ohnologs) retained from WGD ancestral to all salmonids. The major liver cell types showed hundreds of differentially expressed ohnolog pairs, with hepatocytes showing the greatest number and immune cells the least number of uniquely differentially expressed pairs. Many more differentially expressed ohnolog pairs were identified after accounting for cell type heterogeneity within a cell lineage, despite a reduction in statistical power. The degree of conservation in ohnolog expression responses to bacterial infection also varied significantly among cell types, both in terms of the number of differentially expressed pairs and the direction of responses. Overall, this study highlights the importance of resolving cell-specific gene expression to understand the functional and evolutionary outcomes of WGD events.