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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ftunivstirling:oai:dspace.stir.ac.uk:1893/16454 2024-06-02T08:03:19+00:00 Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire Bekaert, Michaël Lowe, Natalie R Bishop, Stephen C Bron, James Taggart, John Houston, Ross D Institute of Aquaculture University of Edinburgh orcid:0000-0002-1206-7654 orcid:0000-0003-3544-0519 orcid:0000-0002-3843-9663 2013-07-29 application/pdf http://hdl.handle.net/1893/16454 https://doi.org/10.1371/journal.pone.0070136 http://dspace.stir.ac.uk/bitstream/1893/16454/1/bekaert_plosone_2013.pdf en eng Public Library of Science Bekaert M, Lowe NR, Bishop SC, Bron J, Taggart J & Houston RD (2013) Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire. PLoS ONE, 8 (7), Art. No.: e70136. https://doi.org/10.1371/journal.pone.0070136 e70136 http://hdl.handle.net/1893/16454 doi:10.1371/journal.pone.0070136 23922936 WOS:000323369700144 2-s2.0-84880793043 685572 http://dspace.stir.ac.uk/bitstream/1893/16454/1/bekaert_plosone_2013.pdf © 2013 Bekaert et al. 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. http://creativecommons.org/licenses/by/4.0/ Salmo salar microRNA aquaculture Journal Article VoR - Version of Record 2013 ftunivstirling https://doi.org/10.1371/journal.pone.0070136 2024-05-07T04:30:11Z 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 University of Stirling: Stirling Digital Research Repository PLoS ONE 8 7 e70136 |
institution |
Open Polar |
collection |
University of Stirling: Stirling Digital Research Repository |
op_collection_id |
ftunivstirling |
language |
English |
topic |
Salmo salar microRNA aquaculture |
spellingShingle |
Salmo salar microRNA aquaculture Bekaert, Michaël Lowe, Natalie R Bishop, Stephen C Bron, James Taggart, John Houston, Ross D Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire |
topic_facet |
Salmo salar microRNA aquaculture |
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. |
author2 |
Institute of Aquaculture University of Edinburgh orcid:0000-0002-1206-7654 orcid:0000-0003-3544-0519 orcid:0000-0002-3843-9663 |
format |
Article in Journal/Newspaper |
author |
Bekaert, Michaël Lowe, Natalie R Bishop, Stephen C Bron, James Taggart, John Houston, Ross D |
author_facet |
Bekaert, Michaël Lowe, Natalie R Bishop, Stephen C Bron, James Taggart, John 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://hdl.handle.net/1893/16454 https://doi.org/10.1371/journal.pone.0070136 http://dspace.stir.ac.uk/bitstream/1893/16454/1/bekaert_plosone_2013.pdf |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Bekaert M, Lowe NR, Bishop SC, Bron J, Taggart J & Houston RD (2013) Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire. PLoS ONE, 8 (7), Art. No.: e70136. https://doi.org/10.1371/journal.pone.0070136 e70136 http://hdl.handle.net/1893/16454 doi:10.1371/journal.pone.0070136 23922936 WOS:000323369700144 2-s2.0-84880793043 685572 http://dspace.stir.ac.uk/bitstream/1893/16454/1/bekaert_plosone_2013.pdf |
op_rights |
© 2013 Bekaert et al. 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. http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1371/journal.pone.0070136 |
container_title |
PLoS ONE |
container_volume |
8 |
container_issue |
7 |
container_start_page |
e70136 |
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1800747813749915648 |