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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ftdoajarticles:oai:doaj.org/article:286d3977046541b6bac9ef25813e8c12 2023-08-27T04:08:28+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 2021-12-01T00:00:00Z https://doi.org/10.3390/biology11010001 https://doaj.org/article/286d3977046541b6bac9ef25813e8c12 EN eng MDPI AG https://www.mdpi.com/2079-7737/11/1/1 https://doaj.org/toc/2079-7737 doi:10.3390/biology11010001 2079-7737 https://doaj.org/article/286d3977046541b6bac9ef25813e8c12 Biology, Vol 11, Iss 1, p 1 (2021) Atlantic salmon smoltification genome mRNAs miRNAs Biology (General) QH301-705.5 article 2021 ftdoajarticles https://doi.org/10.3390/biology11010001 2023-08-06T00:43:13Z 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. Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles Biology 11 1 1 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Atlantic salmon smoltification genome mRNAs miRNAs Biology (General) QH301-705.5 |
spellingShingle |
Atlantic salmon smoltification genome mRNAs miRNAs Biology (General) QH301-705.5 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 |
topic_facet |
Atlantic salmon smoltification genome mRNAs miRNAs Biology (General) QH301-705.5 |
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 |
Article in Journal/Newspaper |
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 |
MDPI AG |
publishDate |
2021 |
url |
https://doi.org/10.3390/biology11010001 https://doaj.org/article/286d3977046541b6bac9ef25813e8c12 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Biology, Vol 11, Iss 1, p 1 (2021) |
op_relation |
https://www.mdpi.com/2079-7737/11/1/1 https://doaj.org/toc/2079-7737 doi:10.3390/biology11010001 2079-7737 https://doaj.org/article/286d3977046541b6bac9ef25813e8c12 |
op_doi |
https://doi.org/10.3390/biology11010001 |
container_title |
Biology |
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11 |
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1 |
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1 |
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1775349278247485440 |