An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)
Background The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physi...
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ftoslouniv:oai:www.duo.uio.no:10852/46687 2023-05-15T15:30:41+02:00 An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar) Hagen-Larsen, Heidi Laerdahl, Jon K Panitz, Frank Adzhubei, Alexei Høyheim, Bjørn 2005 http://hdl.handle.net/10852/46687 http://urn.nb.no/URN:NBN:no-50890 https://doi.org/10.1186/1471-2164-6-171 eng eng http://urn.nb.no/URN:NBN:no-50890 BMC Genomics. 2005 Dec 01;6(1):171 http://hdl.handle.net/10852/46687 http://dx.doi.org/10.1186/1471-2164-6-171 URN:NBN:no-50890 Fulltext https://www.duo.uio.no/bitstream/handle/10852/46687/1/12864_2005_Article_372.pdf Hagen-Larsen et al; licensee BioMed Central Ltd. Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0/ CC-BY Journal article Tidsskriftartikkel Peer reviewed PublishedVersion 2005 ftoslouniv https://doi.org/10.1186/1471-2164-6-171 2020-06-21T08:48:54Z Background The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physiological, morphological and behavioural changes to prepare the salmon for its new environment. These changes are called the parr-smolt transformation or smoltification, and pre-adapt the salmon for survival and growth in the marine environment. The development of hypo-osmotic regulatory ability plays an important part in facilitating the transition from rivers to the sea. The physiological mechanisms behind the developmental changes are largely unknown. An understanding of the transformation process will be vital to the future of the aquaculture industry. A knowledge of which genes are expressed prior to the smoltification process is an important basis for further studies. Results In all, 2974 unique sequences, consisting of 779 contigs and 2195 singlets, were generated for Atlantic salmon from two cDNA libraries constructed from the gills and the intestine, accession numbers [Genbank: CK877169-CK879929, CK884015-CK886537 and CN181112-CN181464]. Nearly 50% of the sequences were assigned putative functions because they showed similarity to known genes, mostly from other species, in one or more of the databases used. The Swiss-Prot database returned significant hits for 1005 sequences. These could be assigned predicted gene products, and 967 were annotated using Gene Ontology (GO) terms for molecular function, biological process and/or cellular component, employing an annotation transfer procedure. Conclusion This paper describes the construction of two cDNA libraries from pre-smolt Atlantic salmon (Salmo salar) and the subsequent EST sequencing, clustering and assigning of putative function to 1005 genes expressed in the gills and/or intestine. Article in Journal/Newspaper Atlantic salmon Salmo salar Universitet i Oslo: Digitale utgivelser ved UiO (DUO) BMC Genomics 6 1 |
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Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
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ftoslouniv |
language |
English |
description |
Background The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physiological, morphological and behavioural changes to prepare the salmon for its new environment. These changes are called the parr-smolt transformation or smoltification, and pre-adapt the salmon for survival and growth in the marine environment. The development of hypo-osmotic regulatory ability plays an important part in facilitating the transition from rivers to the sea. The physiological mechanisms behind the developmental changes are largely unknown. An understanding of the transformation process will be vital to the future of the aquaculture industry. A knowledge of which genes are expressed prior to the smoltification process is an important basis for further studies. Results In all, 2974 unique sequences, consisting of 779 contigs and 2195 singlets, were generated for Atlantic salmon from two cDNA libraries constructed from the gills and the intestine, accession numbers [Genbank: CK877169-CK879929, CK884015-CK886537 and CN181112-CN181464]. Nearly 50% of the sequences were assigned putative functions because they showed similarity to known genes, mostly from other species, in one or more of the databases used. The Swiss-Prot database returned significant hits for 1005 sequences. These could be assigned predicted gene products, and 967 were annotated using Gene Ontology (GO) terms for molecular function, biological process and/or cellular component, employing an annotation transfer procedure. Conclusion This paper describes the construction of two cDNA libraries from pre-smolt Atlantic salmon (Salmo salar) and the subsequent EST sequencing, clustering and assigning of putative function to 1005 genes expressed in the gills and/or intestine. |
format |
Article in Journal/Newspaper |
author |
Hagen-Larsen, Heidi Laerdahl, Jon K Panitz, Frank Adzhubei, Alexei Høyheim, Bjørn |
spellingShingle |
Hagen-Larsen, Heidi Laerdahl, Jon K Panitz, Frank Adzhubei, Alexei Høyheim, Bjørn An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar) |
author_facet |
Hagen-Larsen, Heidi Laerdahl, Jon K Panitz, Frank Adzhubei, Alexei Høyheim, Bjørn |
author_sort |
Hagen-Larsen, Heidi |
title |
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar) |
title_short |
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar) |
title_full |
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar) |
title_fullStr |
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar) |
title_full_unstemmed |
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar) |
title_sort |
est-based approach for identifying genes expressed in the intestine and gills of pre-smolt atlantic salmon (salmo salar) |
publishDate |
2005 |
url |
http://hdl.handle.net/10852/46687 http://urn.nb.no/URN:NBN:no-50890 https://doi.org/10.1186/1471-2164-6-171 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
http://urn.nb.no/URN:NBN:no-50890 BMC Genomics. 2005 Dec 01;6(1):171 http://hdl.handle.net/10852/46687 http://dx.doi.org/10.1186/1471-2164-6-171 URN:NBN:no-50890 Fulltext https://www.duo.uio.no/bitstream/handle/10852/46687/1/12864_2005_Article_372.pdf |
op_rights |
Hagen-Larsen et al; licensee BioMed Central Ltd. Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/1471-2164-6-171 |
container_title |
BMC Genomics |
container_volume |
6 |
container_issue |
1 |
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1766361140186578944 |