Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar )
AbstractChitin 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. Rece...
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Oxford University Press
2023
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ftdoajarticles:oai:doaj.org/article:255dd6e0cb794c26a3e04682f4f6dfc1 2023-07-30T04:02:25+02:00 Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar ) Matilde Mengkrog Holen Gustav Vaaje-Kolstad Matthew Peter Kent Simen Rød Sandve 2023-03-01T00:00:00Z https://doi.org/10.1093/g3journal/jkad069 https://doaj.org/article/255dd6e0cb794c26a3e04682f4f6dfc1 EN eng Oxford University Press https://academic.oup.com/g3journal/article-lookup/doi/10.1093/g3journal/jkad069 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1093/g3journal/jkad069 https://doaj.org/article/255dd6e0cb794c26a3e04682f4f6dfc1 G3: Genes, Genomes, Genetics, Vol 13, Iss 6 (2023) Genetics QH426-470 article 2023 ftdoajarticles https://doi.org/10.1093/g3journal/jkad069 2023-07-09T00:37:10Z AbstractChitin 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 Directory of Open Access Journals: DOAJ Articles G3 Genes|Genomes|Genetics |
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Directory of Open Access Journals: DOAJ Articles |
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language |
English |
topic |
Genetics QH426-470 |
spellingShingle |
Genetics QH426-470 Matilde Mengkrog Holen Gustav Vaaje-Kolstad Matthew Peter Kent Simen Rød Sandve Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon ( Salmo salar ) |
topic_facet |
Genetics QH426-470 |
description |
AbstractChitin 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. |
format |
Article in Journal/Newspaper |
author |
Matilde Mengkrog Holen Gustav Vaaje-Kolstad Matthew Peter Kent Simen Rød Sandve |
author_facet |
Matilde Mengkrog Holen Gustav Vaaje-Kolstad Matthew Peter Kent Simen Rød Sandve |
author_sort |
Matilde Mengkrog Holen |
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 |
publishDate |
2023 |
url |
https://doi.org/10.1093/g3journal/jkad069 https://doaj.org/article/255dd6e0cb794c26a3e04682f4f6dfc1 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
G3: Genes, Genomes, Genetics, Vol 13, Iss 6 (2023) |
op_relation |
https://academic.oup.com/g3journal/article-lookup/doi/10.1093/g3journal/jkad069 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1093/g3journal/jkad069 https://doaj.org/article/255dd6e0cb794c26a3e04682f4f6dfc1 |
op_doi |
https://doi.org/10.1093/g3journal/jkad069 |
container_title |
G3 Genes|Genomes|Genetics |
_version_ |
1772813211624538112 |