Location: Warmwater Aquaculture Research UnitTitle: The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq datasets Author
|Waldbieser, Geoffrey - Geoff|
Submitted to: Biochimica et Biophysica Acta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/22/2014
Publication Date: 4/27/2014
Citation: Zhang, J., Yao, J., Wang, R., Zhang, Y., Liu, S., Sun, L., Jiang, Y., Feng, J., Liu, N., Nelson, D., Waldbieser, G.C., Liu, Z. 2014. The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq datasets. Biochimica et Biophysica Acta. 1840:2813-2828. Interpretive Summary: Annotation of the channel catfish genome sequence assembly is important for the identification of genes that control important traits. Toward that goal, this research focused on the identification of genes encoding cytochrome P450 proteins. A set of 61 cytochrome P450 genes were identified in assembled genomic sequences and genetic probes were used to follow gene expression profiles after infection with bacterial pathogens. The research resulted in molecular tools useful for investigations in toxicological and physiological research in channel catfish.
Technical Abstract: Cytochrome P450s (CYPs) encode one of the most diverse enzyme superfamily in nature. They catalyze oxidative reactions of endogenous molecules and exogenous chemicals. Methods: We identifiedCYPs genes through in silico analysis using EST, RNA-Seq and genome databases of channel catfish.Phylogenetic analyses and conserved syntenic analyses were conducted to determine theiridentities and orthologies. Meta-analysis of RNA-Seq databases was conducted to analyze expression profile of CYP genes following bacterial infection. Results: A full set of 61 CYP geneswere identifiedand characterized in channel catfish. Phylogenetic tree and conserved synteny provided strong evidence of their identities and orthorlogy. Lineage-specific gene duplication was evident in a number of clans in channel catfish. CYP46A1 is missing inthe catfish genome as observed with syntenic analysis and RT-PCR analysis. ThirtyCYPs were found up- or down-regulated in liver, while seven and eight CYPs were observed regulated in intestine and gill following bacterial infection. Conclusion:We systematically identified and characterized a full set of 61 CYP genes in channel catfish and studied their expression profiles after bacterial infection. Strikingly large numbers of CYP genes appear to be involved in the bacterial defense processes. General significance:This work provides an example to systematically study CYP genes in non-model species. Moreover, it provides a basis for further toxicological and physiological studies in channel catfish.