Genome sequence of the olive tree, Olea europaea

Background: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticate...

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Autores: Cruz, Fernando, Julca, Irene, Gómez Garrido, Jèssica, Loska, Damian, Marcet Houben, Marina, Cano, Emilio, Galán Sicilia, Beatriz, Frias, Leonor, Ribeca, Paolo, Derdak, Sophia, Gut, Marta, Sánchez Fernández, Manuel, García, Jose Luis, Gut, Ivo Glynne, Vargas Gómez, Pablo, Alioto, Tyler, Gabaldón Estevan, Juan Antonio, 1973-
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/27611
Acceso en línea:http://hdl.handle.net/10230/27611
http://dx.doi.org/10.1186/s13742-016-0134-5
Access Level:acceso abierto
Palabra clave:Genomics
Assembly
Annotation
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spelling Genome sequence of the olive tree, Olea europaeaCruz, FernandoJulca, IreneGómez Garrido, JèssicaLoska, DamianMarcet Houben, MarinaCano, EmilioGalán Sicilia, BeatrizFrias, LeonorRibeca, PaoloDerdak, SophiaGut, MartaSánchez Fernández, ManuelGarcía, Jose LuisGut, Ivo GlynneVargas Gómez, PabloAlioto, TylerGabaldón Estevan, Juan Antonio, 1973-GenomicsAssemblyAnnotationBackground: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). Findings: A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. Conclusions: The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.BioMed Central201620162016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/27611http://dx.doi.org/10.1186/s13742-016-0134-5reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésGigaScience. 2016;5:29© 2016 The Author(s). Open Access.This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/276112026-06-12T07:21:37Z
dc.title.none.fl_str_mv Genome sequence of the olive tree, Olea europaea
title Genome sequence of the olive tree, Olea europaea
spellingShingle Genome sequence of the olive tree, Olea europaea
Cruz, Fernando
Genomics
Assembly
Annotation
title_short Genome sequence of the olive tree, Olea europaea
title_full Genome sequence of the olive tree, Olea europaea
title_fullStr Genome sequence of the olive tree, Olea europaea
title_full_unstemmed Genome sequence of the olive tree, Olea europaea
title_sort Genome sequence of the olive tree, Olea europaea
dc.creator.none.fl_str_mv Cruz, Fernando
Julca, Irene
Gómez Garrido, Jèssica
Loska, Damian
Marcet Houben, Marina
Cano, Emilio
Galán Sicilia, Beatriz
Frias, Leonor
Ribeca, Paolo
Derdak, Sophia
Gut, Marta
Sánchez Fernández, Manuel
García, Jose Luis
Gut, Ivo Glynne
Vargas Gómez, Pablo
Alioto, Tyler
Gabaldón Estevan, Juan Antonio, 1973-
author Cruz, Fernando
author_facet Cruz, Fernando
Julca, Irene
Gómez Garrido, Jèssica
Loska, Damian
Marcet Houben, Marina
Cano, Emilio
Galán Sicilia, Beatriz
Frias, Leonor
Ribeca, Paolo
Derdak, Sophia
Gut, Marta
Sánchez Fernández, Manuel
García, Jose Luis
Gut, Ivo Glynne
Vargas Gómez, Pablo
Alioto, Tyler
Gabaldón Estevan, Juan Antonio, 1973-
author_role author
author2 Julca, Irene
Gómez Garrido, Jèssica
Loska, Damian
Marcet Houben, Marina
Cano, Emilio
Galán Sicilia, Beatriz
Frias, Leonor
Ribeca, Paolo
Derdak, Sophia
Gut, Marta
Sánchez Fernández, Manuel
García, Jose Luis
Gut, Ivo Glynne
Vargas Gómez, Pablo
Alioto, Tyler
Gabaldón Estevan, Juan Antonio, 1973-
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genomics
Assembly
Annotation
topic Genomics
Assembly
Annotation
description Background: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). Findings: A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. Conclusions: The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.
publishDate 2016
dc.date.none.fl_str_mv 2016
2016
2016
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/27611
http://dx.doi.org/10.1186/s13742-016-0134-5
url http://hdl.handle.net/10230/27611
http://dx.doi.org/10.1186/s13742-016-0134-5
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv GigaScience. 2016;5:29
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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