The cytochrome P450 genes of channel catfish: Their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets

Abstract

Background 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 identified CYPs 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 their identities 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 genes were identified and 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 in the catfish genome as observed with syntenic analysis and RT-PCR analysis. Thirty CYPs 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.

Characterization and sexual dimorphic expression of Cytochrome P450 genes in the hypothalamic–pituitary–gonad axis of yellow catfish

“…Cyp11 and cyp27 genes were clustered together adjacent to the branch of cyp1 and cyp17 genes, and this cluster relation was consistent with the evolutionary status of P450 genes in channel catfish and mammals. Moreover, cyp7 and cyp8 were clustered together in many vertebrates (Eggertsen et al, 1996;Zhang et al, 2014). Similarly, the branches of cyp7 and cyp8 genes were next to the branches of cyp26 and cyp51 genes, and this big cluster was adjacent to the branch of cyp4 and cyp20 genes.…”

The round goby genome provides insights into mechanisms that may facilitate biological invasions

“…Vertebrate genomes contain between 50 and 100 CYP genes. The genomes of fugu (Takifugu rubripes), zebrafish (Danio rerio), and channel catfish (Ictalurus punctatus), for example, encode n = 54 [72], n = 94 [73], and n = 61 [74] CYP genes respectively. Expansions of individual CYP families occur in both mammals and fish.…”

“…5). Fish and most vertebrates have CYP genes from 17 families (CYP 1-5, 7, 8, 11, 17, 19, 20, 21, 24, 26, 27, 46 and 51) [72], while the CYP39 family occurs in humans (Homo sapiens) and zebrafish (Danio rerio), but not in fugu (Takifugu rubripes) or channel catfish (Ictalurus punctatus) [72][73][74]. In the round goby, the complete or partial genes could be assigned to 9 CYP families (CYP 1-4, 8, 19, 26, 27 and 51).…”

How are Bayesian and Non-Parametric Methods Doing a Great Job in RNA-Seq Differential Expression Analysis? : A Review

“…And for an extreme case of gene, a gene has ∼ 1,000 isoform splicing events, suggesting that those isoforms with variability might be more closely related with disease and developmental processes as they generate different protein structure and functionalities, respectively (Beretta et al, 2014;Bernard et al, 2014;Deng et al, 2011;Hiller et al, 2009;Hiller and Wong, 2013;Howard and Heber, 2010;Hu et al, 2014;Jiang and Wong, 2009;Katz et al, 2010;Kaur et al, 2012;Kimes et al, 2014;Lerch et al, 2012;Li et al, 2011;Li and Jiang, 2012;Ma and Zhang, 2013;Mezlini et al, 2013;Mills et al, 2013;Nariai et al, 2013;Nariai et al, 2014;Nicolae et al, 2011;Niu et al, 2014;Patro et al, 2014;Rehrauer et al, 2013;Safikhani et al, 2013;Shi and Jiang, 2013;Suo et al, 2014;Trapnell et al, 2010;Vardhanabhuti et al, 2013;Wang et al, 2010b;Wang et al, 2010c;Wu et al, 2011;Yalamanchili et al, 2014;Zhang et al, 2014).…”

“…With the advent of new elegant count based technology referred to as RNA-seq, newly developed RNA-seq specific methods and adaptively implemented ones from microarrays have been proposed and successfully contributed to transcriptome studies (Gerns Storey et al, 2014;Ginsberg et al, 2010;Han and Jiang, 2014;Kim et al, 2012;Kumar et al, 2012;Li et al, 2014;Mills et al, 2013;Nishiu et al, 2002;Satoh et al, 2014;Wang et al, 2013;Warren et al, 2015;Zhang et al, 2014). Representative statistical methods have been popularly utilized to quantify expression levels of mRNA abundance and identify differentially expressed genes between multiple conditions (Anders and Huber, 2010;Anders et al, 2013;Anders et al, 2012;Bar-Joseph et al, 2012;Bi and Davuluri, 2013;Bullard et al, 2010;Glaus et al, 2012;Hardcastle and Kelly, 2010;Lee et al, 2011;Marioni et al, 2008;Niu et al, 2014;Oh et al, 2013;Oshlack et al, 2010;Pollier et al, 2013;Roberts et al, 2011;Robinson and Oshlack, 2010;Tarazona et al, 2011;Trapnell et al, 2009;Trapnell et al, 2012;Young et al, 2010).…”