Rainbow trout gut and skin microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB38845 | ENA |
REPOSITORIES: ENA
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Project description:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
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Project description:Rainbow trout (Oncorhynchus mykiss), an economically important cold-water fish cultured worldwide, suffers from infectious hematopoietic necrosis virus (IHNV) infection, resulting in huge financial losses. In order to understand the immune response of rainbow trout during virus infection, we explored trout skin transcriptome profiles following IHNV challenge, and identified 6905 differentially expressed genes (DEGs). Transcriptome analysis revealed numerous DEGs involved in immune responses, such as NOD1, NLRC3, NLRC5, TLR3, TLR7/8, TRIM25, DHX58, IFIH1, IRF3/7, STAT1, TRAF3, MX1 and HSP90A1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs were significantly enriched in various immune-related terms including immune system process, innate immune response and regulation of immune effector process and pathways of cytokine-cytokine receptor interactions, NOD-like receptor signaling, RIG-I-like receptor signaling, Toll-like receptor signaling, JAK-STAT signaling, Chemokine signaling pathway, and TNF signaling pathway. In addition, protein-protein interaction network (PPI) was used to display highly interactive DEG networks involving immune-related pathways. The expression trends of 16 DEGs were further verified by quantitative real-time PCR, which confirmed the reliability of the transcriptome sequencing results. This study expands our understanding of the immune response of rainbow trout infected with IHNV, and provides valuable resources for future studies on the immune molecular mechanism and disease resistance breeding.
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