Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation
The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach t...
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ftmdpi:oai:mdpi.com:/2079-7737/11/1/1/ 2023-08-20T04:05:15+02:00 Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation Valentina Valenzuela-Muñoz Cristian Gallardo-Escárate Bárbara P. Benavente Diego Valenzuela-Miranda Gustavo Núñez-Acuña Hugo Escobar-Sepulveda Juan Antonio Váldes agris 2021-12-21 application/pdf https://doi.org/10.3390/biology11010001 EN eng Multidisciplinary Digital Publishing Institute Genetics and Genomics https://dx.doi.org/10.3390/biology11010001 https://creativecommons.org/licenses/by/4.0/ Biology; Volume 11; Issue 1; Pages: 1 Atlantic salmon smoltification genome mRNAs miRNAs Text 2021 ftmdpi https://doi.org/10.3390/biology11010001 2023-08-01T03:36:48Z The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach to analyze complex data sets combining transcriptomes and miRNAs at the chromosome-level genome. Atlantic salmon smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNA and small RNA illumina sequencing. Different expression patterns among the tissues and treatments were observed through a whole-genome transcriptomic approach. Chromosome regions highly expressed between experimental conditions included a great abundance of transposable elements. In addition, differential expression analysis showed a greater number of transcripts modulated in response to SS in gills and head kidney. miRNA expression analysis suggested a small number of miRNAs involved in the smoltification process. However, target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first to evidence the interplaying among mRNAs and miRNAs and the structural relationship at the genome level during Atlantic salmon smoltification. Text Atlantic salmon MDPI Open Access Publishing Biology 11 1 1 |
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English |
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Atlantic salmon smoltification genome mRNAs miRNAs |
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Atlantic salmon smoltification genome mRNAs miRNAs Valentina Valenzuela-Muñoz Cristian Gallardo-Escárate Bárbara P. Benavente Diego Valenzuela-Miranda Gustavo Núñez-Acuña Hugo Escobar-Sepulveda Juan Antonio Váldes Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation |
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Atlantic salmon smoltification genome mRNAs miRNAs |
description |
The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach to analyze complex data sets combining transcriptomes and miRNAs at the chromosome-level genome. Atlantic salmon smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNA and small RNA illumina sequencing. Different expression patterns among the tissues and treatments were observed through a whole-genome transcriptomic approach. Chromosome regions highly expressed between experimental conditions included a great abundance of transposable elements. In addition, differential expression analysis showed a greater number of transcripts modulated in response to SS in gills and head kidney. miRNA expression analysis suggested a small number of miRNAs involved in the smoltification process. However, target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first to evidence the interplaying among mRNAs and miRNAs and the structural relationship at the genome level during Atlantic salmon smoltification. |
format |
Text |
author |
Valentina Valenzuela-Muñoz Cristian Gallardo-Escárate Bárbara P. Benavente Diego Valenzuela-Miranda Gustavo Núñez-Acuña Hugo Escobar-Sepulveda Juan Antonio Váldes |
author_facet |
Valentina Valenzuela-Muñoz Cristian Gallardo-Escárate Bárbara P. Benavente Diego Valenzuela-Miranda Gustavo Núñez-Acuña Hugo Escobar-Sepulveda Juan Antonio Váldes |
author_sort |
Valentina Valenzuela-Muñoz |
title |
Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation |
title_short |
Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation |
title_full |
Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation |
title_fullStr |
Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation |
title_full_unstemmed |
Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation |
title_sort |
whole-genome transcript expression profiling reveals novel insights into transposon genes and non-coding rnas during atlantic salmon seawater adaptation |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2021 |
url |
https://doi.org/10.3390/biology11010001 |
op_coverage |
agris |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Biology; Volume 11; Issue 1; Pages: 1 |
op_relation |
Genetics and Genomics https://dx.doi.org/10.3390/biology11010001 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/biology11010001 |
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Biology |
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11 |
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1 |
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1774715732666351616 |