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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ftpubmed:oai:pubmedcentral.nih.gov:3726450 2023-05-15T15:28:43+02:00 Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire Bekaert, Michaël Lowe, Natalie R. Bishop, Stephen C. Bron, James E. Taggart, John B. Houston, Ross D. 2013-07-29 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726450 http://www.ncbi.nlm.nih.gov/pubmed/23922936 https://doi.org/10.1371/journal.pone.0070136 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726450 http://www.ncbi.nlm.nih.gov/pubmed/23922936 http://dx.doi.org/10.1371/journal.pone.0070136 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2013 ftpubmed https://doi.org/10.1371/journal.pone.0070136 2013-09-05T03:06:53Z 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. Text Atlantic salmon Salmo salar PubMed Central (PMC) PLoS ONE 8 7 e70136 |
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Research Article Bekaert, Michaël Lowe, Natalie R. Bishop, Stephen C. Bron, James E. Taggart, John B. Houston, Ross D. Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire |
topic_facet |
Research Article |
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 |
Text |
author |
Bekaert, Michaël Lowe, Natalie R. Bishop, Stephen C. Bron, James E. Taggart, John B. Houston, Ross D. |
author_facet |
Bekaert, Michaël Lowe, Natalie R. Bishop, Stephen C. Bron, James E. Taggart, John B. Houston, Ross D. |
author_sort |
Bekaert, Michaël |
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 |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726450 http://www.ncbi.nlm.nih.gov/pubmed/23922936 https://doi.org/10.1371/journal.pone.0070136 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726450 http://www.ncbi.nlm.nih.gov/pubmed/23922936 http://dx.doi.org/10.1371/journal.pone.0070136 |
op_rights |
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0070136 |
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PLoS ONE |
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8 |
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7 |
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e70136 |
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1766359052293505024 |