show Abstracthide AbstractHybrid generations usually face either a heterosis advantage or a breakdown that can be expressed by the level of parasite infection in hybrid hosts. Hybrids are less infected by parasites than parental species (especially F1 generations) or more infected than parental species (especially post-F1 generations). We performed the experiment with blood-feeding gill parasite Paradiplozoon homoion (Monogenea) infecting leuciscid species, Abramis brama and Rutilus rutilus, their F1 generation, and two backcross generations. Backcross generations tended to be more parasitized than parental lines and the F1 generation. The number of differentially expressed genes (DEGs) was lower in F1 hybrids and higher in backcross hybrids when compared to each of the parental lines. The main groups of DEGs were shared among lines, however, Abramis brama and Rutilus rutilus differed in some of the top gene ontology (GO) terms. DEG analyses revealed the role of heme binding and erythrocyte differentiation after infection by blood-feeding P. homoion. Two backcross generations shared some of the top GO terms representing mostly downregulated genes associated with P. homoion infection. KEGG analysis revealed the importance of disease-associated pathways. The majority of them were shared by two backcross generations. Our study revealed the most pronounced DEGs associated with monogenean infection in backcross hybrids, potentially explained by hybrid breakdown. The gene expression of F1 hybrids was little affected by P. homoion, suggesting the hybrid advantage. Overall design: Transcriptome profile analyses of head kidney in roach (Rutilus rutilus), common bream (Abramis brama), and their F1 and backcross hybrids to see if infection by monogenean parasites in freshwater fish does reveal differences in fish vigour among parental species and their hybrids. Transcriptomic data includes the fish samples termed using three abbreviations, i.e., K – control samples (samples not exposed to parasite infection), OK - experiment with larval (termed oncomiracidia) infection of Paradiplozoon homoion, and PH – cohabitation experiment with P. homoion (see details below). Each of OK and PH representing independent experiment realized by two different methodologies using the same biological system - the infection by P. homoion (Monogenea) in Abramis brama, Rutilus rutilus and their two F1 generations (F1 generation with A. brama mtDNA, and F1 generation with R. rutilus mtDNA), and two backcross lines (backcross generation of F1 hybrid with A. brama mtDNA and paternal A. brama, and backcross generation of F1 hybrid with A. brama mtDNA and paternal R. rutilus). We performed transcriptome assembly from all the samples of A. brama and R. rutilus, separately. Then, we used the R. rutilus transcriptome for RNA-seq data analyses, including differential expression and functional gene enrichment (GO, KEGG) analyses because it showed better results than the other transcriptome, and at the same time, we avoided complicated cross-referencing. Two experiments (termed OK and PH) with the same biological system were performed. The manuscript associated with the submitted RNA-seq data of both experiments focused, however, only on the analysis of the OK experiment.