First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]

Background: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resourc...

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Autores: Khayi, S., Elhouda Azza, N., Gaboun, F., Pirro, S., Badad, Oussama, Claros, M. Gonzalo, Lightfoot, D. A., Unver, T., Chaouni, B., Merrouch, R., Rahim, B., Essayeh, S., Ganoudi, M., Abdelwahd, R., Diria, G., Mdaghri Alaoui, Mehdi, Labhilili, M., Iraqi, D., Mouhaddab, J., Sedrati, H., Memari, M., Hamamouch, N., Alché Ramírez, Juan de Dios, Boukhatem, N., Mrabet, R., Dahan, R., Legssyer, A., Khalfaoui, M., Badraoui, M., Vande Peer, Y., Tatusova, T., El Mousadik, A., Mentag, R., Ghazal, Hassan
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2018
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/216948
Acceso en línea:http://hdl.handle.net/10261/216948
Access Level:acceso abierto
Palabra clave:Argane
Argania spinosa
Endemic
Genome
Assembly
Morocco
International Argane Genome Consortium
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repository_id_str
spelling First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]Khayi, S.Elhouda Azza, N.Gaboun, F.Pirro, S.Badad, OussamaClaros, M. GonzaloLightfoot, D. A.Unver, T.Chaouni, B.Merrouch, R.Rahim, B.Essayeh, S.Ganoudi, M.Abdelwahd, R.Diria, G.Mdaghri Alaoui, MehdiLabhilili, M.Iraqi, D.Mouhaddab, J.Sedrati, H.Memari, M.Hamamouch, N.Alché Ramírez, Juan de DiosBoukhatem, N.Mrabet, R.Dahan, R.Legssyer, A.Khalfaoui, M.Badraoui, M.Vande Peer, Y.Tatusova, T.El Mousadik, A.Mentag, R.Ghazal, HassanArganeArgania spinosaEndemicGenomeAssemblyMoroccoInternational Argane Genome ConsortiumBackground: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.2 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3% of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological purposes.This work was supported by the Iridian Genome Foundation (MD, USA). H.G. is supported by a Grant from the NIH (MD, USA) for H3ABioNet/H3Africa (grant numbers U41HG006941 and U24 HG006941). O.B. and B.C. are Fulbright JSD (USA) grant recipients. This work also benefited from support of Midterm Research Program of INRA-Morocco through the use of its bioinformatics platform.Fulbright CommissionIridian Genome FoundationConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2020202020182020info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/216948reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.12688/F1000RESEARCH.15719.1Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2169482026-05-22T06:33:51Z
dc.title.none.fl_str_mv First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
title First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
spellingShingle First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
Khayi, S.
Argane
Argania spinosa
Endemic
Genome
Assembly
Morocco
International Argane Genome Consortium
title_short First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
title_full First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
title_fullStr First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
title_full_unstemmed First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
title_sort First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]
dc.creator.none.fl_str_mv Khayi, S.
Elhouda Azza, N.
Gaboun, F.
Pirro, S.
Badad, Oussama
Claros, M. Gonzalo
Lightfoot, D. A.
Unver, T.
Chaouni, B.
Merrouch, R.
Rahim, B.
Essayeh, S.
Ganoudi, M.
Abdelwahd, R.
Diria, G.
Mdaghri Alaoui, Mehdi
Labhilili, M.
Iraqi, D.
Mouhaddab, J.
Sedrati, H.
Memari, M.
Hamamouch, N.
Alché Ramírez, Juan de Dios
Boukhatem, N.
Mrabet, R.
Dahan, R.
Legssyer, A.
Khalfaoui, M.
Badraoui, M.
Vande Peer, Y.
Tatusova, T.
El Mousadik, A.
Mentag, R.
Ghazal, Hassan
author Khayi, S.
author_facet Khayi, S.
Elhouda Azza, N.
Gaboun, F.
Pirro, S.
Badad, Oussama
Claros, M. Gonzalo
Lightfoot, D. A.
Unver, T.
Chaouni, B.
Merrouch, R.
Rahim, B.
Essayeh, S.
Ganoudi, M.
Abdelwahd, R.
Diria, G.
Mdaghri Alaoui, Mehdi
Labhilili, M.
Iraqi, D.
Mouhaddab, J.
Sedrati, H.
Memari, M.
Hamamouch, N.
Alché Ramírez, Juan de Dios
Boukhatem, N.
Mrabet, R.
Dahan, R.
Legssyer, A.
Khalfaoui, M.
Badraoui, M.
Vande Peer, Y.
Tatusova, T.
El Mousadik, A.
Mentag, R.
Ghazal, Hassan
author_role author
author2 Elhouda Azza, N.
Gaboun, F.
Pirro, S.
Badad, Oussama
Claros, M. Gonzalo
Lightfoot, D. A.
Unver, T.
Chaouni, B.
Merrouch, R.
Rahim, B.
Essayeh, S.
Ganoudi, M.
Abdelwahd, R.
Diria, G.
Mdaghri Alaoui, Mehdi
Labhilili, M.
Iraqi, D.
Mouhaddab, J.
Sedrati, H.
Memari, M.
Hamamouch, N.
Alché Ramírez, Juan de Dios
Boukhatem, N.
Mrabet, R.
Dahan, R.
Legssyer, A.
Khalfaoui, M.
Badraoui, M.
Vande Peer, Y.
Tatusova, T.
El Mousadik, A.
Mentag, R.
Ghazal, Hassan
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Fulbright Commission
Iridian Genome Foundation
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Argane
Argania spinosa
Endemic
Genome
Assembly
Morocco
International Argane Genome Consortium
topic Argane
Argania spinosa
Endemic
Genome
Assembly
Morocco
International Argane Genome Consortium
description Background: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.2 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3% of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological purposes.
publishDate 2018
dc.date.none.fl_str_mv 2018
2020
2020
2020
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/10261/216948
url http://hdl.handle.net/10261/216948
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.12688/F1000RESEARCH.15719.1
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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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