Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration

• DOI: 10.1371/journal.pone.0300472
• Publication Date: 2024-03-22T17:32:27Z
• Authors: Cláudia Raposo de...; Kenneth Sandoval; Ferenc Kagan; Grace McCormack; Denise Schrama; Raquel Carrilho; Ana Paula Farinha; Marco Cerqueira; Pedro M. Rodrigues
• Keywords: RNA-Seq

Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance raising issues related to sustainability, animal welfare, food safety. The advent next-generation sequencing technologies has greatly revolutionized the study stress biology, allowing a deeper understanding molecular responses. Here, we characterized for first time, using RNA-seq, different hepatic transcriptome responses gilthead common aquaculture challenges, namely overcrowding, net handling, hypoxia, further integrating them with liver proteome metabolome After reference-guided assembly, annotation, differential gene expression analysis, 7, 343, 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) from hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR 0.05) suggested scenario challenge-specific responses, that is, handling induced ribosomal assembly whereas DNA replication hepatocytes, consistent proteomics metabolomics' results. However, both converged upon downregulation insulin growth factor signalling induction endoplasmic reticulum stress. These results demonstrate high phenotypic plasticity this distinct challenging environments at transcriptomic level. Furthermore, it provides significant resources characterizing identifying potentially novel are resilience efficiency regard welfare.