Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire.
Atlantic salmon (Salmo salar L.), a member of the family Salmonidae, is a totemic species of ecological and cultural significance that is also economically important in terms of both sports fisheries and aquaculture. These factors have promoted the continuous development of genomic resources for thi...
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ftdoajarticles:oai:doaj.org/article:2dae7dde19c44db987aaa261375c5f70 2023-05-15T15:28:43+02:00 Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire. Michaël Bekaert Natalie R Lowe Stephen C Bishop James E Bron John B Taggart Ross D Houston 2013-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0070136 https://doaj.org/article/2dae7dde19c44db987aaa261375c5f70 EN eng Public Library of Science (PLoS) https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23922936/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0070136 https://doaj.org/article/2dae7dde19c44db987aaa261375c5f70 PLoS ONE, Vol 8, Iss 7, p e70136 (2013) Medicine R Science Q article 2013 ftdoajarticles https://doi.org/10.1371/journal.pone.0070136 2022-12-31T15:11:39Z Atlantic salmon (Salmo salar L.), a member of the family Salmonidae, is a totemic species of ecological and cultural significance that is also economically important in terms of both sports fisheries and aquaculture. These factors have promoted the continuous development of genomic resources for this species, furthering both fundamental and applied research. MicroRNAs (miRNA) are small endogenous non-coding RNA molecules that control spatial and temporal expression of targeted genes through post-transcriptional regulation. While miRNA have been characterised in detail for many other species, this is not yet the case for Atlantic salmon. To identify miRNAs from Atlantic salmon, we constructed whole fish miRNA libraries for 18 individual juveniles (fry, four months post hatch) and characterised them by Illumina high-throughput sequencing (total of 354,505,167 paired-ended reads). We report an extensive and partly novel repertoire of miRNA sequences, comprising 888 miRNA genes (547 unique mature miRNA sequences), quantify their expression levels in basal conditions, examine their homology to miRNAs from other species and identify their predicted target genes. We also identify the location and putative copy number of the miRNA genes in the draft Atlantic salmon reference genome sequence. The Atlantic salmon miRNAs experimentally identified in this study provide a robust large-scale resource for functional genome research in salmonids. There is an opportunity to explore the evolution of salmonid miRNAs following the relatively recent whole genome duplication event in salmonid species and to investigate the role of miRNAs in the regulation of gene expression in particular their contribution to variation in economically and ecologically important traits. Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles PLoS ONE 8 7 e70136 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Michaël Bekaert Natalie R Lowe Stephen C Bishop James E Bron John B Taggart Ross D Houston Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire. |
topic_facet |
Medicine R Science Q |
description |
Atlantic salmon (Salmo salar L.), a member of the family Salmonidae, is a totemic species of ecological and cultural significance that is also economically important in terms of both sports fisheries and aquaculture. These factors have promoted the continuous development of genomic resources for this species, furthering both fundamental and applied research. MicroRNAs (miRNA) are small endogenous non-coding RNA molecules that control spatial and temporal expression of targeted genes through post-transcriptional regulation. While miRNA have been characterised in detail for many other species, this is not yet the case for Atlantic salmon. To identify miRNAs from Atlantic salmon, we constructed whole fish miRNA libraries for 18 individual juveniles (fry, four months post hatch) and characterised them by Illumina high-throughput sequencing (total of 354,505,167 paired-ended reads). We report an extensive and partly novel repertoire of miRNA sequences, comprising 888 miRNA genes (547 unique mature miRNA sequences), quantify their expression levels in basal conditions, examine their homology to miRNAs from other species and identify their predicted target genes. We also identify the location and putative copy number of the miRNA genes in the draft Atlantic salmon reference genome sequence. The Atlantic salmon miRNAs experimentally identified in this study provide a robust large-scale resource for functional genome research in salmonids. There is an opportunity to explore the evolution of salmonid miRNAs following the relatively recent whole genome duplication event in salmonid species and to investigate the role of miRNAs in the regulation of gene expression in particular their contribution to variation in economically and ecologically important traits. |
format |
Article in Journal/Newspaper |
author |
Michaël Bekaert Natalie R Lowe Stephen C Bishop James E Bron John B Taggart Ross D Houston |
author_facet |
Michaël Bekaert Natalie R Lowe Stephen C Bishop James E Bron John B Taggart Ross D Houston |
author_sort |
Michaël Bekaert |
title |
Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire. |
title_short |
Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire. |
title_full |
Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire. |
title_fullStr |
Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire. |
title_full_unstemmed |
Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire. |
title_sort |
sequencing and characterisation of an extensive atlantic salmon (salmo salar l.) microrna repertoire. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2013 |
url |
https://doi.org/10.1371/journal.pone.0070136 https://doaj.org/article/2dae7dde19c44db987aaa261375c5f70 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
PLoS ONE, Vol 8, Iss 7, p e70136 (2013) |
op_relation |
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23922936/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0070136 https://doaj.org/article/2dae7dde19c44db987aaa261375c5f70 |
op_doi |
https://doi.org/10.1371/journal.pone.0070136 |
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PLoS ONE |
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8 |
container_issue |
7 |
container_start_page |
e70136 |
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1766359052628000768 |