Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)

RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads i...

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Autores: Sánchez-Sevilla, José F, Vallarino, José G, Osorio, Sonia, Bombarely, Aureliano, Posé, David, Merchante, Catharina, Botella, Miguel A, Amaya, Iraida, Valpuesta, Victoriano
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/416422
Acceso en línea:http://hdl.handle.net/10261/416422
https://api.elsevier.com/content/abstract/scopus_id/85032180998
Access Level:acceso abierto
Palabra clave:Fragaria × ananassa
RNA-seq
Strawberry
Fruit ripening
Atlas
Transcriptome assembly
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spelling Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)Sánchez-Sevilla, José FVallarino, José GOsorio, SoniaBombarely, AurelianoPosé, DavidMerchante, CatharinaBotella, Miguel AAmaya, IraidaValpuesta, VictorianoFragaria × ananassaRNA-seqStrawberryFruit ripeningAtlasTranscriptome assemblyRNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample.The project was funded by the Grant BIO2013-44199-R (MINECO, Spain) and Grant ERC-2014-StG 638134; SO and DP were supported by the Ramón and Cajal program (MINECO-Universidad de Málaga, Spain) (Grants RYC-09170 and RYC-2013-1269)Peer reviewedSpringer NatureUniversidad de MálagaBombarely, Aureliano [0000-0001-6257-8914]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262017info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/416422https://api.elsevier.com/content/abstract/scopus_id/85032180998reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO//BIO2013-44199-Rinfo:eu-repo/grantAgreement/MINECO//RYC-2013-12699The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1038/s41598-017-14239-6https://doi.org/10.1038/s41598-017-14239-6Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/4164222026-05-22T06:33:51Z
dc.title.none.fl_str_mv Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
title Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
spellingShingle Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
Sánchez-Sevilla, José F
Fragaria × ananassa
RNA-seq
Strawberry
Fruit ripening
Atlas
Transcriptome assembly
title_short Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
title_full Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
title_fullStr Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
title_full_unstemmed Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
title_sort Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
dc.creator.none.fl_str_mv Sánchez-Sevilla, José F
Vallarino, José G
Osorio, Sonia
Bombarely, Aureliano
Posé, David
Merchante, Catharina
Botella, Miguel A
Amaya, Iraida
Valpuesta, Victoriano
author Sánchez-Sevilla, José F
author_facet Sánchez-Sevilla, José F
Vallarino, José G
Osorio, Sonia
Bombarely, Aureliano
Posé, David
Merchante, Catharina
Botella, Miguel A
Amaya, Iraida
Valpuesta, Victoriano
author_role author
author2 Vallarino, José G
Osorio, Sonia
Bombarely, Aureliano
Posé, David
Merchante, Catharina
Botella, Miguel A
Amaya, Iraida
Valpuesta, Victoriano
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidad de Málaga
Bombarely, Aureliano [0000-0001-6257-8914]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Fragaria × ananassa
RNA-seq
Strawberry
Fruit ripening
Atlas
Transcriptome assembly
topic Fragaria × ananassa
RNA-seq
Strawberry
Fruit ripening
Atlas
Transcriptome assembly
description RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample.
publishDate 2017
dc.date.none.fl_str_mv 2017
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/416422
https://api.elsevier.com/content/abstract/scopus_id/85032180998
url http://hdl.handle.net/10261/416422
https://api.elsevier.com/content/abstract/scopus_id/85032180998
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO//BIO2013-44199-R
info:eu-repo/grantAgreement/MINECO//RYC-2013-12699
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1038/s41598-017-14239-6
https://doi.org/10.1038/s41598-017-14239-6
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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repository.mail.fl_str_mv
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