Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensi...

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Detalhes bibliográficos
Autores: González-Ibeas, Daniel, Martínez-García, Pedro J., Famula, Randi A., Delfino-Mix, Annette, Stevens, Kristian A., Loopstra, Carol A., Langley, Charles H., Neale, David B., Wegrzyn, Jill L.
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/339172
Acesso em linha:http://hdl.handle.net/10261/339172
Access Level:acceso abierto
Palavra-chave:Conifer
Transcriptome
Dicer
Gymnosperm
DCL
RNA-Seq
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spelling Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)González-Ibeas, DanielMartínez-García, Pedro J.Famula, Randi A.Delfino-Mix, AnnetteStevens, Kristian A.Loopstra, Carol A.Langley, Charles H.Neale, David B.Wegrzyn, Jill L.ConiferTranscriptomeDicerGymnospermDCLRNA-SeqSugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifersWe thank Pacific Biosciences for their support for library construction and Jeffrey Puryear (Texas A&M University) for sample preparation and RNA extraction. This work was supported by United States Department of Agriculture/National Institute of Food and Agriculture (USDA/NIFA #2011-67009-30030) within the framework of the PineRefSeq project (http://pinegenome.org/pinerefseq/)Peer reviewedOxford University PressNational Institute of Food and Agriculture (US)Martínez-García, Pedro J. [0000-0002-7647-5235]202320232016info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/339172reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésThe underlying dataset has been published as supplementary material of the article in the publisher platform at doi:10.1534/g3.116.032805/-/DC1https://doi.org/10.1534/g3.116.032805Noinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3391722026-05-22T06:33:51Z
dc.title.none.fl_str_mv Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
title Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
spellingShingle Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
González-Ibeas, Daniel
Conifer
Transcriptome
Dicer
Gymnosperm
DCL
RNA-Seq
title_short Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
title_full Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
title_fullStr Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
title_full_unstemmed Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
title_sort Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
dc.creator.none.fl_str_mv González-Ibeas, Daniel
Martínez-García, Pedro J.
Famula, Randi A.
Delfino-Mix, Annette
Stevens, Kristian A.
Loopstra, Carol A.
Langley, Charles H.
Neale, David B.
Wegrzyn, Jill L.
author González-Ibeas, Daniel
author_facet González-Ibeas, Daniel
Martínez-García, Pedro J.
Famula, Randi A.
Delfino-Mix, Annette
Stevens, Kristian A.
Loopstra, Carol A.
Langley, Charles H.
Neale, David B.
Wegrzyn, Jill L.
author_role author
author2 Martínez-García, Pedro J.
Famula, Randi A.
Delfino-Mix, Annette
Stevens, Kristian A.
Loopstra, Carol A.
Langley, Charles H.
Neale, David B.
Wegrzyn, Jill L.
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv National Institute of Food and Agriculture (US)
Martínez-García, Pedro J. [0000-0002-7647-5235]
dc.subject.none.fl_str_mv Conifer
Transcriptome
Dicer
Gymnosperm
DCL
RNA-Seq
topic Conifer
Transcriptome
Dicer
Gymnosperm
DCL
RNA-Seq
description Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers
publishDate 2016
dc.date.none.fl_str_mv 2016
2023
2023
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/10261/339172
url http://hdl.handle.net/10261/339172
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv The underlying dataset has been published as supplementary material of the article in the publisher platform at doi:10.1534/g3.116.032805/-/DC1
https://doi.org/10.1534/g3.116.032805
No
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
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
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.228081

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