The chemical defensome of fish

Interspecies differences in sensitivity to chemical exposures pose a great challenge in toxicological risk assessments. How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Although the types of defensome genes are generally conserved in animals, there are important differences in the complement and function of specific genes between species. Being the largest group of vertebrate species, teleost fish can provide valuable insight into the evolution and functional diversity of defensome genes.

In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch and are often used as model species in toxicological studies and environmental monitoring programs, including Zebrafish (Danio rerio), Atlantic cod (Gadus morhua), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus) and stickleback (Gasterosteus aculeatus). Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how the species sense and respond to environmental pollutants. Furthermore, we show that there are important differences in expression of chemical defense genes between stickleback and zebrafish during early development. The results indicate that the diversity and function of the defensome will be important for toxicological testing and risk assessments studies.

DOI: 10.15490/fairdomhub.1.study.424.1

Zenodo URL: None

Created at: 16th Dec 2020 at 23:48

Contents

Chemical defensome genes for five fish species

Build the chemical defensome gene list for 5 fish: Zebrafish (Danio rerio), Atlantic cod (Gadus morhua), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus) and stickleback (Gasterosteus aculeatus). Source code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/defensomeGenes

Chemical defensome relevant Pfam accession list

No description specified

  • Pfam-defensome_accession_list.txt

Gene pattern to filter defensome relevant genes

There are four datasheets in the Excel file: 1. Gene pattern and the corresponding category (the gene list is then divided into the other three datasheets); 2. These gene names (patterns) can be directly followed by either a letter or a number; 3. These gene names (patterns) should be directly followed by a letter; 4. These gene names (patterns) should be directly followed by a number.

  • defensome_gene_pattern.xlsx

Chemical defensome genes overview for five fish

No description specified

  • Chemical defensome genes overview.xlsx

Supplementary_Table1_Table2

Supplementary Table1 and Table2 for manuscript "The chemical defensome of fish"

  • The chemical defensome of fish_Supplementary_Table1_Table2.docx

Expression of defensome genes in early development of fish

To study the defensome genes' expression in early developmental stages of zebrafish and stickleback. Souce code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/developmentalStages

Exposure response of defensome genes

Exposing zebrafish to benzo(a)pyrene (B(a)P) (gene counts from NCBI GEO: GSE64198, previously published by Fang, et al. 2015. Souce code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/exposureResponse

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Citation
Söderström, S., Eide, M., Zhang, X., Karlsen, O. A., Goksøyr, A., & Jonassen, I. (2020). The chemical defensome of fish. FAIRDOMHub. https://doi.org/10.15490/FAIRDOMHUB.1.STUDY.424.1
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Created: 16th Dec 2020 at 23:48

Last updated: 16th Dec 2020 at 23:48

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