Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish
- Autores
- Palstra, Arjan P.; Beltran, Sergi; Burgerhout, Erik; Brittijn, Sebastiaan A.; Magnoni, Leonardo Julián; Henkel, Christiaan V.; Jansen, Hans J.; Van Den Thillart, Guido E. E. J. M.; Spaink, Herman P.; Planas, Josep V.
- Año de publicación
- 2013
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming-induced exercise. Pubertal autumn-spawning seawater-raised female rainbow trout were rested (n = 10) or swum (n = 10) for 1176 km at 0.75 body-lengths per second in a 6,000-L swimflume under reproductive conditions for 40 days. Red and white muscle RNA of exercised and non-exercised fish (4 lanes) was sequenced and resulted in 15–17 million reads per lane that, after de novo assembly, yielded 149,159 red and 118,572 white muscle contigs. Most contigs were annotated using an iterative homology search strategy against salmonid ESTs, the zebrafish Danio rerio genome and general Metazoan genes. When selecting for large contigs (.500 nucleotides), a number of novel rainbow trout gene sequences were identified in this study: 1,085 and 1,228 novel gene sequences for red and white muscle, respectively, which included a number of important molecules for skeletal muscle function. Transcriptomic analysis revealed that sustained swimming increased transcriptional activity in skeletal muscle and specifically an upregulation of genes involved in muscle growth and developmental processes in white muscle. The unique collection of transcripts will contribute to our understanding of red and white muscle physiology, specifically during the long-term reproductive migration of salmonids.
Fil: Palstra, Arjan P.. Universidad de Barcelona. Facultad de Biología; España;
Fil: Beltran, Sergi. Universidad de Barcelona; España
Fil: Burgerhout, Erik. No especifíca;
Fil: Brittijn, Sebastiaan A.. No especifíca;
Fil: Magnoni, Leonardo Julián. Universidad de Barcelona; España. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Henkel, Christiaan V.. No especifíca;
Fil: Jansen, Hans J.. No especifíca;
Fil: Van Den Thillart, Guido E. E. J. M.. No especifíca;
Fil: Spaink, Herman P.. No especifíca;
Fil: Planas, Josep V.. Universidad de Barcelona; España - Materia
-
Skeletal Muscle Transcriptome
Endurance Exercise
Fish Physiology
Rna Sequencing - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/2422
Ver los metadatos del registro completo
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oai:ri.conicet.gov.ar:11336/2422 |
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CONICET Digital (CONICET) |
spelling |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming FishPalstra, Arjan P.Beltran, SergiBurgerhout, ErikBrittijn, Sebastiaan A.Magnoni, Leonardo JuliánHenkel, Christiaan V.Jansen, Hans J.Van Den Thillart, Guido E. E. J. M.Spaink, Herman P.Planas, Josep V.Skeletal Muscle TranscriptomeEndurance ExerciseFish PhysiologyRna Sequencinghttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming-induced exercise. Pubertal autumn-spawning seawater-raised female rainbow trout were rested (n = 10) or swum (n = 10) for 1176 km at 0.75 body-lengths per second in a 6,000-L swimflume under reproductive conditions for 40 days. Red and white muscle RNA of exercised and non-exercised fish (4 lanes) was sequenced and resulted in 15–17 million reads per lane that, after de novo assembly, yielded 149,159 red and 118,572 white muscle contigs. Most contigs were annotated using an iterative homology search strategy against salmonid ESTs, the zebrafish Danio rerio genome and general Metazoan genes. When selecting for large contigs (.500 nucleotides), a number of novel rainbow trout gene sequences were identified in this study: 1,085 and 1,228 novel gene sequences for red and white muscle, respectively, which included a number of important molecules for skeletal muscle function. Transcriptomic analysis revealed that sustained swimming increased transcriptional activity in skeletal muscle and specifically an upregulation of genes involved in muscle growth and developmental processes in white muscle. The unique collection of transcripts will contribute to our understanding of red and white muscle physiology, specifically during the long-term reproductive migration of salmonids.Fil: Palstra, Arjan P.. Universidad de Barcelona. Facultad de Biología; España;Fil: Beltran, Sergi. Universidad de Barcelona; EspañaFil: Burgerhout, Erik. No especifíca;Fil: Brittijn, Sebastiaan A.. No especifíca;Fil: Magnoni, Leonardo Julián. Universidad de Barcelona; España. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Henkel, Christiaan V.. No especifíca;Fil: Jansen, Hans J.. No especifíca;Fil: Van Den Thillart, Guido E. E. J. M.. No especifíca;Fil: Spaink, Herman P.. No especifíca;Fil: Planas, Josep V.. Universidad de Barcelona; EspañaPublic Library of Science2013-01-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/2422Palstra, Arjan P.; Beltran, Sergi; Burgerhout, Erik; Brittijn, Sebastiaan A.; Magnoni, Leonardo Julián; et al.; Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish; Public Library of Science; Plos One; 8; 1; 8-1-2013; 1-141932-6203enginfo:eu-repo/semantics/altIdentifier/doi/DOI:10.1371/journal.pone.0053171info:eu-repo/semantics/altIdentifier/url/http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540090/info:eu-repo/semantics/altIdentifier/url/http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053171info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:08:30Zoai:ri.conicet.gov.ar:11336/2422instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:08:30.939CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish |
title |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish |
spellingShingle |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish Palstra, Arjan P. Skeletal Muscle Transcriptome Endurance Exercise Fish Physiology Rna Sequencing |
title_short |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish |
title_full |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish |
title_fullStr |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish |
title_full_unstemmed |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish |
title_sort |
Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish |
dc.creator.none.fl_str_mv |
Palstra, Arjan P. Beltran, Sergi Burgerhout, Erik Brittijn, Sebastiaan A. Magnoni, Leonardo Julián Henkel, Christiaan V. Jansen, Hans J. Van Den Thillart, Guido E. E. J. M. Spaink, Herman P. Planas, Josep V. |
author |
Palstra, Arjan P. |
author_facet |
Palstra, Arjan P. Beltran, Sergi Burgerhout, Erik Brittijn, Sebastiaan A. Magnoni, Leonardo Julián Henkel, Christiaan V. Jansen, Hans J. Van Den Thillart, Guido E. E. J. M. Spaink, Herman P. Planas, Josep V. |
author_role |
author |
author2 |
Beltran, Sergi Burgerhout, Erik Brittijn, Sebastiaan A. Magnoni, Leonardo Julián Henkel, Christiaan V. Jansen, Hans J. Van Den Thillart, Guido E. E. J. M. Spaink, Herman P. Planas, Josep V. |
author2_role |
author author author author author author author author author |
dc.subject.none.fl_str_mv |
Skeletal Muscle Transcriptome Endurance Exercise Fish Physiology Rna Sequencing |
topic |
Skeletal Muscle Transcriptome Endurance Exercise Fish Physiology Rna Sequencing |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming-induced exercise. Pubertal autumn-spawning seawater-raised female rainbow trout were rested (n = 10) or swum (n = 10) for 1176 km at 0.75 body-lengths per second in a 6,000-L swimflume under reproductive conditions for 40 days. Red and white muscle RNA of exercised and non-exercised fish (4 lanes) was sequenced and resulted in 15–17 million reads per lane that, after de novo assembly, yielded 149,159 red and 118,572 white muscle contigs. Most contigs were annotated using an iterative homology search strategy against salmonid ESTs, the zebrafish Danio rerio genome and general Metazoan genes. When selecting for large contigs (.500 nucleotides), a number of novel rainbow trout gene sequences were identified in this study: 1,085 and 1,228 novel gene sequences for red and white muscle, respectively, which included a number of important molecules for skeletal muscle function. Transcriptomic analysis revealed that sustained swimming increased transcriptional activity in skeletal muscle and specifically an upregulation of genes involved in muscle growth and developmental processes in white muscle. The unique collection of transcripts will contribute to our understanding of red and white muscle physiology, specifically during the long-term reproductive migration of salmonids. Fil: Palstra, Arjan P.. Universidad de Barcelona. Facultad de Biología; España; Fil: Beltran, Sergi. Universidad de Barcelona; España Fil: Burgerhout, Erik. No especifíca; Fil: Brittijn, Sebastiaan A.. No especifíca; Fil: Magnoni, Leonardo Julián. Universidad de Barcelona; España. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Henkel, Christiaan V.. No especifíca; Fil: Jansen, Hans J.. No especifíca; Fil: Van Den Thillart, Guido E. E. J. M.. No especifíca; Fil: Spaink, Herman P.. No especifíca; Fil: Planas, Josep V.. Universidad de Barcelona; España |
description |
Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming-induced exercise. Pubertal autumn-spawning seawater-raised female rainbow trout were rested (n = 10) or swum (n = 10) for 1176 km at 0.75 body-lengths per second in a 6,000-L swimflume under reproductive conditions for 40 days. Red and white muscle RNA of exercised and non-exercised fish (4 lanes) was sequenced and resulted in 15–17 million reads per lane that, after de novo assembly, yielded 149,159 red and 118,572 white muscle contigs. Most contigs were annotated using an iterative homology search strategy against salmonid ESTs, the zebrafish Danio rerio genome and general Metazoan genes. When selecting for large contigs (.500 nucleotides), a number of novel rainbow trout gene sequences were identified in this study: 1,085 and 1,228 novel gene sequences for red and white muscle, respectively, which included a number of important molecules for skeletal muscle function. Transcriptomic analysis revealed that sustained swimming increased transcriptional activity in skeletal muscle and specifically an upregulation of genes involved in muscle growth and developmental processes in white muscle. The unique collection of transcripts will contribute to our understanding of red and white muscle physiology, specifically during the long-term reproductive migration of salmonids. |
publishDate |
2013 |
dc.date.none.fl_str_mv |
2013-01-08 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/2422 Palstra, Arjan P.; Beltran, Sergi; Burgerhout, Erik; Brittijn, Sebastiaan A.; Magnoni, Leonardo Julián; et al.; Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish; Public Library of Science; Plos One; 8; 1; 8-1-2013; 1-14 1932-6203 |
url |
http://hdl.handle.net/11336/2422 |
identifier_str_mv |
Palstra, Arjan P.; Beltran, Sergi; Burgerhout, Erik; Brittijn, Sebastiaan A.; Magnoni, Leonardo Julián; et al.; Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish; Public Library of Science; Plos One; 8; 1; 8-1-2013; 1-14 1932-6203 |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/DOI:10.1371/journal.pone.0053171 info:eu-repo/semantics/altIdentifier/url/http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540090/ info:eu-repo/semantics/altIdentifier/url/http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053171 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Public Library of Science |
publisher.none.fl_str_mv |
Public Library of Science |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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