Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes
Osmoregulatory capabilities have played an important role in the evolution, dispersal, and diversification of vertebrates. To better understand the genetic architecture of hypo-osmoregulation in fishes and to determine which genes and biological processes affect intraspecific variation in salinity t...
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ftpubmed:oai:pubmedcentral.nih.gov:3921346 2023-05-15T14:30:07+02:00 Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. 2013-12-24 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921346 http://www.ncbi.nlm.nih.gov/pubmed/24368751 https://doi.org/10.1152/physiolgenomics.00105.2013 en eng American Physiological Society http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/24368751 http://dx.doi.org/10.1152/physiolgenomics.00105.2013 Copyright © 2014 the American Physiological Society Call for Papers: NextGen Sequencing-based Dissection of Physiological Systems Text 2013 ftpubmed https://doi.org/10.1152/physiolgenomics.00105.2013 2015-02-22T00:52:37Z Osmoregulatory capabilities have played an important role in the evolution, dispersal, and diversification of vertebrates. To better understand the genetic architecture of hypo-osmoregulation in fishes and to determine which genes and biological processes affect intraspecific variation in salinity tolerance, we used mRNA sequence libraries from Arctic charr gill tissue to compare gene expression profiles in fish exhibiting divergent salinity tolerance quantitative trait locus (QTL) genotypes. We compared differentially expressed genes with QTL positions to gain insight about the nature of the underlying polymorphisms and examined gene expression within the context of genome organization to gain insight about the evolution of hypo-osmoregulation in fishes. mRNA sequencing of 18 gill tissue libraries produced 417 million reads, and the final reduced de novo transcriptome assembly consisted of 92,543 contigs. Families contained a similar number of differentially expressed contigs between high and low salinity tolerance capacity groups, and log2 expression ratios ranged from 10.4 to −8.6. We found that intraspecific variation in salinity tolerance capacity correlated with differential expression of immune response genes. Some differentially expressed genes formed clusters along linkage groups. Most clusters comprised gene pairs, though clusters of three, four, and eight genes were also observed. We postulated that conserved synteny of gene clusters on multiple ancestral and teleost chromosomes may have been preserved via purifying selection. Colocalization of QTL with differentially expressed genes suggests that polymorphisms in cis-regulatory elements are part of a majority of QTL. Text Arctic charr Arctic Salvelinus alpinus PubMed Central (PMC) Arctic Physiological Genomics 46 4 123 137 |
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Call for Papers: NextGen Sequencing-based Dissection of Physiological Systems |
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Call for Papers: NextGen Sequencing-based Dissection of Physiological Systems Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes |
topic_facet |
Call for Papers: NextGen Sequencing-based Dissection of Physiological Systems |
description |
Osmoregulatory capabilities have played an important role in the evolution, dispersal, and diversification of vertebrates. To better understand the genetic architecture of hypo-osmoregulation in fishes and to determine which genes and biological processes affect intraspecific variation in salinity tolerance, we used mRNA sequence libraries from Arctic charr gill tissue to compare gene expression profiles in fish exhibiting divergent salinity tolerance quantitative trait locus (QTL) genotypes. We compared differentially expressed genes with QTL positions to gain insight about the nature of the underlying polymorphisms and examined gene expression within the context of genome organization to gain insight about the evolution of hypo-osmoregulation in fishes. mRNA sequencing of 18 gill tissue libraries produced 417 million reads, and the final reduced de novo transcriptome assembly consisted of 92,543 contigs. Families contained a similar number of differentially expressed contigs between high and low salinity tolerance capacity groups, and log2 expression ratios ranged from 10.4 to −8.6. We found that intraspecific variation in salinity tolerance capacity correlated with differential expression of immune response genes. Some differentially expressed genes formed clusters along linkage groups. Most clusters comprised gene pairs, though clusters of three, four, and eight genes were also observed. We postulated that conserved synteny of gene clusters on multiple ancestral and teleost chromosomes may have been preserved via purifying selection. Colocalization of QTL with differentially expressed genes suggests that polymorphisms in cis-regulatory elements are part of a majority of QTL. |
format |
Text |
author |
Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. |
author_facet |
Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. |
author_sort |
Norman, Joseph D. |
title |
Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes |
title_short |
Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes |
title_full |
Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes |
title_fullStr |
Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes |
title_full_unstemmed |
Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes |
title_sort |
transcriptomics of salinity tolerance capacity in arctic charr (salvelinus alpinus): a comparison of gene expression profiles between divergent qtl genotypes |
publisher |
American Physiological Society |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921346 http://www.ncbi.nlm.nih.gov/pubmed/24368751 https://doi.org/10.1152/physiolgenomics.00105.2013 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Salvelinus alpinus |
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Arctic charr Arctic Salvelinus alpinus |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/24368751 http://dx.doi.org/10.1152/physiolgenomics.00105.2013 |
op_rights |
Copyright © 2014 the American Physiological Society |
op_doi |
https://doi.org/10.1152/physiolgenomics.00105.2013 |
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Physiological Genomics |
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46 |
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4 |
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123 |
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137 |
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