Promising efforts are ongoing to extend genomics resources for pikeperch (Sander lucioperca), a species of high interest for sustainable European aquaculture sector. Although previous work, including reference genome assembly, transcriptome sequences, and single-nucleotide polymorphism genotyping, added a great wealth of genomic tools, a comprehensive characterization of spatiotemporal gene expression across major tissues in pikeperch is still needed. Here, we used deep RNA-Sequencing of ten vital tissues collected in eight animals, to build a high-confident and annotated trancriptome atlas, to detect the tissue specificity of gene expression and co-expression modules, and to investigate selective signatures in the pikeperch genome. Pathway enrichment and protein-protein interaction network analyses were performed to characterize the unique biological functions of tissue-specific genes and co-expression modules. We found strong tissue correlations and similarities with respect to their expression pattern, e.g., head kidney and spleen, or gills and skin--- but also significant differences in the complexity and composition of their transcriptomes. Moreover, functional analyses revealed that tissue-specific genes essentially play key roles in the specific physiological functions of the respective tissues. Although tissue specificity was not associated with positive selection, several genes under positive selection were found to be involved in hypoxia, immunity, and gene regulation (transcription factors) processes, which are crucial for fish adaption and welfare. Overall, these new resources and findings will not only enhance the understanding of mechanisms of organ biology in pikeperch, but also complement the amount of genomic insights on this aquaculture species.
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