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Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar)

Matilde Mengkrog Holen, View ORCID ProfileMatthew Peter Kent, View ORCID ProfileGustav Vaaje-Kolstad, View ORCID ProfileSimen Rød Sandve
doi: https://doi.org/10.1101/2022.05.05.490710
Matilde Mengkrog Holen
1Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
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Matthew Peter Kent
1Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
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Gustav Vaaje-Kolstad
2Department of Chemistry, Biotechnology and Food Science (IKBM), Norwegian University of Life Sciences, NO-1432 Ås, Norway
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Simen Rød Sandve
1Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
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  • For correspondence: simen.sandve@nmbu.no
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ABSTRACT

Background Chitin is one of the most abundant polysaccharides in nature, forming important structures in insects, crustaceans, and fungal cell walls. Vertebrates on the other hand are generally considered “non-chitinous” organisms, despite having highly conserved chitin metabolism associated genes. Recent work has revealed that the largest group of vertebrates, the teleosts, have the potential to both synthesize and degrade endogenous chitin. Yet little is still known about the genes and proteins responsible for these dynamic processes. Here we used comparative genomics, transcriptomics, and chromatin accessibility data to characterize the repertoire, evolution, and regulation of genes involved in chitin-metabolism in teleosts, with a particular focus on Atlantic salmon.

Results Reconstruction of gene family phylogenies provide evidence for an expansion of teleost and salmonid chitinase and chitin synthase genes after multiple whole-genome duplications. Analyses of multi-tissue gene expression data demonstrated a strong bias of gastrointestinal tract expression for chitin metabolism genes, but with different spatial and temporal tissue specificities. Finally, we integrated transcriptomes from a developmental time series of the gastrointestinal tract with chromatin accessibility data to identify putative transcription factors responsible for regulating chitin-metabolism gene expression (CDX1 and CDX2) as well as tissue-specific divergence in the regulation of gene duplicates (FOXJ2). These transcription factors are also potential regulators of multiple glycosyltransferases being co-expressed with the chitin remodeling genes.

Conclusion The findings presented here add support to the hypothesis that chitin metabolism genes in teleosts play a role in developing and maintaining a chitin-based barrier in the teleost gut and provide a basis for further investigations into the molecular basis of this barrier.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8959/

  • https://www.ncbi.nlm.nih.gov/bioproject/72713

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB21981

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB24480

  • https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8306/

  • https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9001/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 05, 2022.
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Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar)
Matilde Mengkrog Holen, Matthew Peter Kent, Gustav Vaaje-Kolstad, Simen Rød Sandve
bioRxiv 2022.05.05.490710; doi: https://doi.org/10.1101/2022.05.05.490710
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Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar)
Matilde Mengkrog Holen, Matthew Peter Kent, Gustav Vaaje-Kolstad, Simen Rød Sandve
bioRxiv 2022.05.05.490710; doi: https://doi.org/10.1101/2022.05.05.490710

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