Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar)
Abstract 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 “nonchitinous” organisms, despite having highly conserved chitin metabolism-associated genes. Rec...
Published in: | G3 Genes|Genomes|Genetics |
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Oxford University Press (OUP)
2023
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croxfordunivpr:10.1093/g3journal/jkad069 2024-05-19T07:37:41+00:00 Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar) Holen, Matilde Mengkrog Vaaje-Kolstad, Gustav Kent, Matthew Peter Sandve, Simen Rød Yáñez, J 2023 http://dx.doi.org/10.1093/g3journal/jkad069 https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkad069/49651789/jkad069.pdf https://academic.oup.com/g3journal/article-pdf/13/6/jkad069/56716340/jkad069.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by/4.0/ G3: Genes, Genomes, Genetics volume 13, issue 6 ISSN 2160-1836 journal-article 2023 croxfordunivpr https://doi.org/10.1093/g3journal/jkad069 2024-05-02T09:29:41Z Abstract 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 “nonchitinous” 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 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. Reconstruction of gene family phylogenies provides 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). The findings presented here support 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Oxford University Press G3 Genes|Genomes|Genetics |
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Open Polar |
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Oxford University Press |
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croxfordunivpr |
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English |
description |
Abstract 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 “nonchitinous” 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 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. Reconstruction of gene family phylogenies provides 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). The findings presented here support 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. |
author2 |
Yáñez, J |
format |
Article in Journal/Newspaper |
author |
Holen, Matilde Mengkrog Vaaje-Kolstad, Gustav Kent, Matthew Peter Sandve, Simen Rød |
spellingShingle |
Holen, Matilde Mengkrog Vaaje-Kolstad, Gustav Kent, Matthew Peter Sandve, Simen Rød Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar) |
author_facet |
Holen, Matilde Mengkrog Vaaje-Kolstad, Gustav Kent, Matthew Peter Sandve, Simen Rød |
author_sort |
Holen, Matilde Mengkrog |
title |
Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar) |
title_short |
Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar) |
title_full |
Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar) |
title_fullStr |
Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar) |
title_full_unstemmed |
Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar) |
title_sort |
gene family expansion and functional diversification of chitinase and chitin synthase genes in atlantic salmon ( salmo salar) |
publisher |
Oxford University Press (OUP) |
publishDate |
2023 |
url |
http://dx.doi.org/10.1093/g3journal/jkad069 https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkad069/49651789/jkad069.pdf https://academic.oup.com/g3journal/article-pdf/13/6/jkad069/56716340/jkad069.pdf |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
G3: Genes, Genomes, Genetics volume 13, issue 6 ISSN 2160-1836 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1093/g3journal/jkad069 |
container_title |
G3 Genes|Genomes|Genetics |
_version_ |
1799477019992391680 |