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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23922936/pdf/?tool=EBI |
| _version_ | 1819280885125480448 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-24T00:50:54Z |
| format | Article |
| id | doaj.art-2dae7dde19c44db987aaa261375c5f70 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-24T00:50:54Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2dae7dde19c44db987aaa261375c5f702022-12-21T17:23:35ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e7013610.1371/journal.pone.0070136Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire.Michaël BekaertNatalie R LoweStephen C BishopJames E BronJohn B TaggartRoss D HoustonAtlantic 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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23922936/pdf/?tool=EBI |
| spellingShingle | 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. PLoS ONE |
| title | 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_short | 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23922936/pdf/?tool=EBI |
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