The cytochrome P450 genes of channel catfish

Their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets

Jiaren Zhang, Jun Yao, Ruijia Wang, Yu Zhang, Shikai Liu, Luyang Sun, Yanliang Jiang, Jianbin Feng, Nannan Liu, David Nelson, Geoff Waldbieser, Zhanjiang Liu

Research output: Contribution to journalArticle

13 Citations (Scopus)

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 was 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. While bacterial challenge altered the expression of large numbers of CYP genes, the mechanisms and significance of these changes are not known. 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.

Original languageEnglish (US)
Pages (from-to)2813-2828
Number of pages16
JournalBiochimica et Biophysica Acta - General Subjects
Volume1840
Issue number9
DOIs
StatePublished - Jan 1 2014

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Ictaluridae
Cytochromes
Cytochrome P-450 Enzyme System
Meta-Analysis
Genes
RNA
Bacterial Infections
Genome
Synteny
Datasets
Catfishes
Gene Duplication
Expressed Sequence Tags
Nucleic Acid Databases
Liver
Computer Simulation
Toxicology
Intestines
Databases
Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

The cytochrome P450 genes of channel catfish : Their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets. / Zhang, Jiaren; Yao, Jun; Wang, Ruijia; Zhang, Yu; Liu, Shikai; Sun, Luyang; Jiang, Yanliang; Feng, Jianbin; Liu, Nannan; Nelson, David; Waldbieser, Geoff; Liu, Zhanjiang.

In: Biochimica et Biophysica Acta - General Subjects, Vol. 1840, No. 9, 01.01.2014, p. 2813-2828.

Research output: Contribution to journalArticle

Zhang, Jiaren ; Yao, Jun ; Wang, Ruijia ; Zhang, Yu ; Liu, Shikai ; Sun, Luyang ; Jiang, Yanliang ; Feng, Jianbin ; Liu, Nannan ; Nelson, David ; Waldbieser, Geoff ; Liu, Zhanjiang. / The cytochrome P450 genes of channel catfish : Their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets. In: Biochimica et Biophysica Acta - General Subjects. 2014 ; Vol. 1840, No. 9. pp. 2813-2828.
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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 was 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. While bacterial challenge altered the expression of large numbers of CYP genes, the mechanisms and significance of these changes are not known. 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.",
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AB - 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 was 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. While bacterial challenge altered the expression of large numbers of CYP genes, the mechanisms and significance of these changes are not known. 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.

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