De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus.
[EN] The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene mo...
| Autores: | , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2018 |
| País: | España |
| Institución: | Universitat Politècnica de València (UPV) |
| Repositorio: | RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
| Idioma: | inglés |
| OAI Identifier: | oai:riunet.upv.es:10251/200879 |
| Acceso en línea: | https://riunet.upv.es/handle/10251/200879 |
| Access Level: | acceso abierto |
| Palabra clave: | Genome Crop Zucchini Whole genome duplication Cucurbitaceae Transcriptome BOTANICA GENETICA |
| id |
ES_4facd2f39be86cf3c796cb720c98cb48 |
|---|---|
| oai_identifier_str |
oai:riunet.upv.es:10251/200879 |
| network_acronym_str |
ES |
| network_name_str |
España |
| repository_id_str |
|
| spelling |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus.Montero-Pau, JavierBombarely, AurelianoZiarsolo, PeioMartí-Gomez, CarlosGómez, PedroJamilena, ManuelMueller, LukasBlanca Postigo, José Miguel|||0000-0002-5884-8624Esteras Gómez, Cristina|||0000-0002-8789-4363Ferriol Molina, María|||0000-0002-6533-5720Picó Sirvent, María Belén|||0000-0001-7761-990XCañizares Sales, Joaquín|||0000-0001-9002-5516GenomeCropZucchiniWhole genome duplicationCucurbitaceaeTranscriptomeBOTANICAGENETICA[EN] The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 +/- 4 Mya in the ancestral species that gave rise to the genus.This work was partially funded by the INIA project RTA2011-00044-C02-2 with contributions of E-RTA2013-00020-C04-03 of the Spanish Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) cofunded with FEDER funds (EU) and AGL2014-54598-C2-1-R of the Spanish Ministry of Economy and Competitivity. The authors declare no conflict of interest.Blackwell PublishingDepartamento de Ecosistemas AgroforestalesDepartamento de BiotecnologíaInstituto Universitario de Conservación y Mejora de la Agrodiversidad ValencianaInstituto Agroforestal MediterráneoEscuela Técnica Superior de Ingeniería Agronómica y del Medio NaturalEuropean Regional Development FundMinisterio de Economía y CompetitividadInstituto Nacional de Investigación y Tecnología Agraria y AlimentariaRepositorio Institucional de la Universitat Politècnica de València Riunet20182018-06-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://riunet.upv.es/handle/10251/200879reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengMinisterio de Ciencia e Innovación http://dx.doi.org/10.13039/501100004837 RTA2011-00044-C02-02 Desarrollo competitivo de nuevos cultivares de calabacín y ampliación de la plataforma genómica para la mejora de esta hortalizaMinisterio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 AGL2014-54598-C2-1-R DESARROLLO DE HERRAMIENTAS FISIOLOGICAS Y GENOMICAS PARA LA MEJORA DE LA CALIDAD POSTCOSECHA DEL FRUTO DE CALABACINMinisterio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 RTA2013-00020-C04-03 Identificación de resistencias a ToLCNDV en Cucurbitáceas y análisis genético de las mismasopen accesshttp://purl.org/coar/access_right/c_abf2Reconocimiento (by)http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/2008792026-06-13T07:49:27Z |
| dc.title.none.fl_str_mv |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. |
| title |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. |
| spellingShingle |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. Montero-Pau, Javier Genome Crop Zucchini Whole genome duplication Cucurbitaceae Transcriptome BOTANICA GENETICA |
| title_short |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. |
| title_full |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. |
| title_fullStr |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. |
| title_full_unstemmed |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. |
| title_sort |
De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. |
| dc.creator.none.fl_str_mv |
Montero-Pau, Javier Bombarely, Aureliano Ziarsolo, Peio Martí-Gomez, Carlos Gómez, Pedro Jamilena, Manuel Mueller, Lukas Blanca Postigo, José Miguel|||0000-0002-5884-8624 Esteras Gómez, Cristina|||0000-0002-8789-4363 Ferriol Molina, María|||0000-0002-6533-5720 Picó Sirvent, María Belén|||0000-0001-7761-990X Cañizares Sales, Joaquín|||0000-0001-9002-5516 |
| author |
Montero-Pau, Javier |
| author_facet |
Montero-Pau, Javier Bombarely, Aureliano Ziarsolo, Peio Martí-Gomez, Carlos Gómez, Pedro Jamilena, Manuel Mueller, Lukas Blanca Postigo, José Miguel|||0000-0002-5884-8624 Esteras Gómez, Cristina|||0000-0002-8789-4363 Ferriol Molina, María|||0000-0002-6533-5720 Picó Sirvent, María Belén|||0000-0001-7761-990X Cañizares Sales, Joaquín|||0000-0001-9002-5516 |
| author_role |
author |
| author2 |
Bombarely, Aureliano Ziarsolo, Peio Martí-Gomez, Carlos Gómez, Pedro Jamilena, Manuel Mueller, Lukas Blanca Postigo, José Miguel|||0000-0002-5884-8624 Esteras Gómez, Cristina|||0000-0002-8789-4363 Ferriol Molina, María|||0000-0002-6533-5720 Picó Sirvent, María Belén|||0000-0001-7761-990X Cañizares Sales, Joaquín|||0000-0001-9002-5516 |
| author2_role |
author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Departamento de Ecosistemas Agroforestales Departamento de Biotecnología Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana Instituto Agroforestal Mediterráneo Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural European Regional Development Fund Ministerio de Economía y Competitividad Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria Repositorio Institucional de la Universitat Politècnica de València Riunet |
| dc.subject.none.fl_str_mv |
Genome Crop Zucchini Whole genome duplication Cucurbitaceae Transcriptome BOTANICA GENETICA |
| topic |
Genome Crop Zucchini Whole genome duplication Cucurbitaceae Transcriptome BOTANICA GENETICA |
| description |
[EN] The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 +/- 4 Mya in the ancestral species that gave rise to the genus. |
| publishDate |
2018 |
| dc.date.none.fl_str_mv |
2018 2018-06-01 |
| dc.type.none.fl_str_mv |
journal article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://riunet.upv.es/handle/10251/200879 |
| url |
https://riunet.upv.es/handle/10251/200879 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.relation.none.fl_str_mv |
Ministerio de Ciencia e Innovación http://dx.doi.org/10.13039/501100004837 RTA2011-00044-C02-02 Desarrollo competitivo de nuevos cultivares de calabacín y ampliación de la plataforma genómica para la mejora de esta hortaliza Ministerio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 AGL2014-54598-C2-1-R DESARROLLO DE HERRAMIENTAS FISIOLOGICAS Y GENOMICAS PARA LA MEJORA DE LA CALIDAD POSTCOSECHA DEL FRUTO DE CALABACIN Ministerio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 RTA2013-00020-C04-03 Identificación de resistencias a ToLCNDV en Cucurbitáceas y análisis genético de las mismas |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Reconocimiento (by) http://creativecommons.org/licenses/by/4.0/ |
| dc.rights.openaire.fl_str_mv |
info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Reconocimiento (by) http://creativecommons.org/licenses/by/4.0/ |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
| dc.publisher.none.fl_str_mv |
Blackwell Publishing |
| publisher.none.fl_str_mv |
Blackwell Publishing |
| dc.source.none.fl_str_mv |
reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia instname:Universitat Politècnica de València (UPV) |
| instname_str |
Universitat Politècnica de València (UPV) |
| reponame_str |
RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
| collection |
RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
| repository.name.fl_str_mv |
|
| repository.mail.fl_str_mv |
|
| _version_ |
1869407834366541824 |
| score |
15,300719 |