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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Autores principales:	Michaël Bekaert, Natalie R Lowe, Stephen C Bishop, James E Bron, John B Taggart, Ross D Houston
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2dae7dde19c44db987aaa261375c5f70
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spelling	oai:doaj.org-article:2dae7dde19c44db987aaa261375c5f702021-11-18T09:02:14ZSequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire.1932-620310.1371/journal.pone.0070136https://doaj.org/article/2dae7dde19c44db987aaa261375c5f702013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23922936/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Atlantic 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.Michaël BekaertNatalie R LoweStephen C BishopJames E BronJohn B TaggartRoss D HoustonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e70136 (2013)
institution	DOAJ
collection	DOAJ
language	EN
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.
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
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://doaj.org/article/2dae7dde19c44db987aaa261375c5f70
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Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire.

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