An improved assembly and annotation of the melon (Cucumis melo L.) reference genome

We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecul...

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Autores: Ruggieri, Valentino|||0000-0001-6038-8703, Alexiou, Konstantinos G.|||0000-0003-0121-9517, Morata, Jordi|||0000-0002-6146-4322, Argyris, Jason|||0000-0003-2685-9959, Pujol Abajo, Marta|||0000-0002-3595-5363, Yano, Ryoichi, Nonaka, Satoko, Ezura, Hiroshi, Latrasse, David, Boualem, Adnane, Benhamed, Moussa, Bendahmane, Abdelhafid|||0000-0003-3246-868X, Aiese Cigliano, Riccardo|||0000-0002-9058-6994, Sanseverino, Walter|||0000-0003-3324-5912, Puigdomènech, Pere|||0000-0002-9866-861X, Casacuberta, Josep M.|||0000-0002-5609-4152, Garcia-Mas, Jordi|||0000-0001-7101-9049
Tipo de recurso: artículo
Fecha de publicación:2018
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:200508
Acceso en línea:https://ddd.uab.cat/record/200508
https://dx.doi.org/urn:doi:10.1038/s41598-018-26416-2
Access Level:acceso abierto
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spelling An improved assembly and annotation of the melon (Cucumis melo L.) reference genomeRuggieri, Valentino|||0000-0001-6038-8703Alexiou, Konstantinos G.|||0000-0003-0121-9517Morata, Jordi|||0000-0002-6146-4322Argyris, Jason|||0000-0003-2685-9959Pujol Abajo, Marta|||0000-0002-3595-5363Yano, RyoichiNonaka, SatokoEzura, HiroshiLatrasse, DavidBoualem, AdnaneBenhamed, MoussaBendahmane, Abdelhafid|||0000-0003-3246-868XAiese Cigliano, Riccardo|||0000-0002-9058-6994Sanseverino, Walter|||0000-0003-3324-5912Puigdomènech, Pere|||0000-0002-9866-861XCasacuberta, Josep M.|||0000-0002-5609-4152Garcia-Mas, Jordi|||0000-0001-7101-9049We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species. 22018-01-0120182018-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/200508https://dx.doi.org/urn:doi:10.1038/s41598-018-26416-2reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengMinisterio de Economía y Competitividad https://doi.org/10.13039/501100003329 AGL2015-64625-C2-1-RMinisterio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2015-0533European Commission https://doi.org/10.13039/501100000780 6655919open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2005082026-06-06T12:50:31Z
dc.title.none.fl_str_mv An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
title An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
spellingShingle An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
Ruggieri, Valentino|||0000-0001-6038-8703
title_short An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
title_full An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
title_fullStr An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
title_full_unstemmed An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
title_sort An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
dc.creator.none.fl_str_mv Ruggieri, Valentino|||0000-0001-6038-8703
Alexiou, Konstantinos G.|||0000-0003-0121-9517
Morata, Jordi|||0000-0002-6146-4322
Argyris, Jason|||0000-0003-2685-9959
Pujol Abajo, Marta|||0000-0002-3595-5363
Yano, Ryoichi
Nonaka, Satoko
Ezura, Hiroshi
Latrasse, David
Boualem, Adnane
Benhamed, Moussa
Bendahmane, Abdelhafid|||0000-0003-3246-868X
Aiese Cigliano, Riccardo|||0000-0002-9058-6994
Sanseverino, Walter|||0000-0003-3324-5912
Puigdomènech, Pere|||0000-0002-9866-861X
Casacuberta, Josep M.|||0000-0002-5609-4152
Garcia-Mas, Jordi|||0000-0001-7101-9049
author Ruggieri, Valentino|||0000-0001-6038-8703
author_facet Ruggieri, Valentino|||0000-0001-6038-8703
Alexiou, Konstantinos G.|||0000-0003-0121-9517
Morata, Jordi|||0000-0002-6146-4322
Argyris, Jason|||0000-0003-2685-9959
Pujol Abajo, Marta|||0000-0002-3595-5363
Yano, Ryoichi
Nonaka, Satoko
Ezura, Hiroshi
Latrasse, David
Boualem, Adnane
Benhamed, Moussa
Bendahmane, Abdelhafid|||0000-0003-3246-868X
Aiese Cigliano, Riccardo|||0000-0002-9058-6994
Sanseverino, Walter|||0000-0003-3324-5912
Puigdomènech, Pere|||0000-0002-9866-861X
Casacuberta, Josep M.|||0000-0002-5609-4152
Garcia-Mas, Jordi|||0000-0001-7101-9049
author_role author
author2 Alexiou, Konstantinos G.|||0000-0003-0121-9517
Morata, Jordi|||0000-0002-6146-4322
Argyris, Jason|||0000-0003-2685-9959
Pujol Abajo, Marta|||0000-0002-3595-5363
Yano, Ryoichi
Nonaka, Satoko
Ezura, Hiroshi
Latrasse, David
Boualem, Adnane
Benhamed, Moussa
Bendahmane, Abdelhafid|||0000-0003-3246-868X
Aiese Cigliano, Riccardo|||0000-0002-9058-6994
Sanseverino, Walter|||0000-0003-3324-5912
Puigdomènech, Pere|||0000-0002-9866-861X
Casacuberta, Josep M.|||0000-0002-5609-4152
Garcia-Mas, Jordi|||0000-0001-7101-9049
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
description We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.
publishDate 2018
dc.date.none.fl_str_mv 2
2018-01-01
2018
2018-01-01
dc.type.none.fl_str_mv 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://ddd.uab.cat/record/200508
https://dx.doi.org/urn:doi:10.1038/s41598-018-26416-2
url https://ddd.uab.cat/record/200508
https://dx.doi.org/urn:doi:10.1038/s41598-018-26416-2
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 AGL2015-64625-C2-1-R
Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2015-0533
European Commission https://doi.org/10.13039/501100000780 6655919
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://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
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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