Multi-tissue transcriptome profiling of north American derived Atlantic salmon
The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing are enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analyzed transcriptomes from se...
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ftunivqespace:oai:espace.library.uq.edu.au:UQ:219b6a6 2023-05-15T15:30:17+02:00 Multi-tissue transcriptome profiling of north American derived Atlantic salmon Mohamed, Amin R. King, Harry Evans, Bradley Reverter, Antonio Kijas, James W. 2018-09-13 https://espace.library.uq.edu.au/view/UQ:219b6a6 eng eng Frontiers Research Foundation doi:10.3389/fgene.2018.00369 issn:1664-8021 Atlantic salmon Gene expression Next-gen sequencing RNA-Seq Transcription factors Transcriptome 1311 Genetics 1313 Molecular Medicine 2716 Genetics (clinical) Journal Article 2018 ftunivqespace https://doi.org/10.3389/fgene.2018.00369 2020-10-20T01:10:04Z The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing are enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analyzed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from pituitary gland, brain, ovary, and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting, and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. We identified a cluster of 508 tissue specific genes for pituitary gland, 3395 for brain, 2939 for ovary, and 539 for liver. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors (TFs) present in each tissue-specific gene cluster were identified. TFs belonging to homeobox and bhlh families were identified for pituitary gland, pou and zf-c2h2 families for brain, arid, and zf-c2h2 for ovary and rxr-like family for liver. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation. Article in Journal/Newspaper Atlantic salmon Salmo salar The University of Queensland: UQ eSpace Frontiers in Genetics 9 |
institution |
Open Polar |
collection |
The University of Queensland: UQ eSpace |
op_collection_id |
ftunivqespace |
language |
English |
topic |
Atlantic salmon Gene expression Next-gen sequencing RNA-Seq Transcription factors Transcriptome 1311 Genetics 1313 Molecular Medicine 2716 Genetics (clinical) |
spellingShingle |
Atlantic salmon Gene expression Next-gen sequencing RNA-Seq Transcription factors Transcriptome 1311 Genetics 1313 Molecular Medicine 2716 Genetics (clinical) Mohamed, Amin R. King, Harry Evans, Bradley Reverter, Antonio Kijas, James W. Multi-tissue transcriptome profiling of north American derived Atlantic salmon |
topic_facet |
Atlantic salmon Gene expression Next-gen sequencing RNA-Seq Transcription factors Transcriptome 1311 Genetics 1313 Molecular Medicine 2716 Genetics (clinical) |
description |
The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing are enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analyzed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from pituitary gland, brain, ovary, and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting, and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. We identified a cluster of 508 tissue specific genes for pituitary gland, 3395 for brain, 2939 for ovary, and 539 for liver. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors (TFs) present in each tissue-specific gene cluster were identified. TFs belonging to homeobox and bhlh families were identified for pituitary gland, pou and zf-c2h2 families for brain, arid, and zf-c2h2 for ovary and rxr-like family for liver. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation. |
format |
Article in Journal/Newspaper |
author |
Mohamed, Amin R. King, Harry Evans, Bradley Reverter, Antonio Kijas, James W. |
author_facet |
Mohamed, Amin R. King, Harry Evans, Bradley Reverter, Antonio Kijas, James W. |
author_sort |
Mohamed, Amin R. |
title |
Multi-tissue transcriptome profiling of north American derived Atlantic salmon |
title_short |
Multi-tissue transcriptome profiling of north American derived Atlantic salmon |
title_full |
Multi-tissue transcriptome profiling of north American derived Atlantic salmon |
title_fullStr |
Multi-tissue transcriptome profiling of north American derived Atlantic salmon |
title_full_unstemmed |
Multi-tissue transcriptome profiling of north American derived Atlantic salmon |
title_sort |
multi-tissue transcriptome profiling of north american derived atlantic salmon |
publisher |
Frontiers Research Foundation |
publishDate |
2018 |
url |
https://espace.library.uq.edu.au/view/UQ:219b6a6 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.3389/fgene.2018.00369 issn:1664-8021 |
op_doi |
https://doi.org/10.3389/fgene.2018.00369 |
container_title |
Frontiers in Genetics |
container_volume |
9 |
_version_ |
1766360737098235904 |