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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/2422

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oai_identifier_str oai:ri.conicet.gov.ar:11336/2422
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str 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
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv 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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