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An improved reference genome and first organelle genomes of Quercus suber

2023-11Journal article Open access
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dc.contributor.authorUsié, Ana
dc.contributor.authorSerra, Octávio
dc.contributor.authorBarros, Pedro M.
dc.contributor.authorBarbosa, Pedro
dc.contributor.authorLeão, Célia
dc.contributor.authorCapote, Tiago
dc.contributor.authorAlmeida, Tânia
dc.contributor.authorRodrigues, Leandra
dc.contributor.authorCarrasquinho, Isabel
dc.contributor.authorGuimarães, Joana B.
dc.contributor.authorMendoça, Diogo
dc.contributor.authorNóbrega, Filomena
dc.contributor.authorEgas, Conceição
dc.contributor.authorChaves, Inês
dc.contributor.authorAbreu, Isabel A.
dc.contributor.authorSaibo, Nelson J. M.
dc.contributor.authorMarum, Liliana
dc.contributor.authorVarela, Maria Carolina
dc.contributor.authorMatos, José
dc.contributor.authorSimões, Fernanda
dc.contributor.authorMiguel, Célia M.
dc.contributor.authorOliveira, M. Margarida
dc.contributor.authorRicardo, Cândido P.
dc.contributor.authorGonçalves, Sónia
dc.contributor.authorRamos, António Marcos
dc.date.accessioned2024-03-15T12:26:29Z
dc.date.available2024-03-15T12:26:29Z
dc.date.issued2023-11
dc.description.abstractCork oak (Quercus suber L.) is an ecologically and economically important evergreen tree species native to the Mediterranean region and widespread in southwest Europe and northwest Africa. An improved genome assembly of cork oak using a combination of Illumina and PacBio sequencing is presented in this study. The assembled genome contains 2351 scaffolds longer than 1000 bp, accounting for 765.7 Mbp of genome size, L90 of 755, and a N50 of 1.0 Mbp, with 40,131 annotated genes. The repetitive sequences constitute 53.6% of the genome. The genome sequences of chloroplast and mitochondrion were determined for the first time, with a genome size of 161,179 bp and 531,858 bp, respectively. Phylogenetic analysis based on complete chloroplast genome sequence showed that Q. suber is closely related to Quercus variabilis, two cork-producing species with commercial use. All data generated are available through the public databases, being ready to be used without restrictions. This study provides an improved nuclear genome assembly together with the organelle genomes of cork oak. These resources will be useful for further breeding strategies and conservation programs and for comparative genomic studies in oak species.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationUsié, A., Serra, O., Barros, P.M. et al. An improved reference genome and first organelle genomes of Quercus suber. Tree Genetics & Genomes 19, 54 (2023). https://doi.org/10.1007/s11295-023-01624-8pt_PT
dc.identifier.doi10.1007/s11295-023-01624-8pt_PT
dc.identifier.urihttp://hdl.handle.net/10451/63447
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherSpringerpt_PT
dc.relationInAlentejo under the scope of “GenoSuber–Cork oak genome sequencing” (ALENT-07-0224-FEDER-001754), and by Alentejo2020, through FEDER under the scope “Lentidev-A genomic approach to cork quality” (ALT20-03-0145-FEDER-000020) and by Program PORTUGAL 2020 Partnership Agreement, under the scope of Biodata.pt–Infraestrutura Portuguesa de Dados Biológicos (22231/01/SAICT/2016), through the European Regional Development Fund (ERDF)pt_PT
dc.relation(FCT), I.P., is acknowledged for funding researchers: Contrato–Programa to L. Marum (CEECINST/00131/2018), Contrato–Programa to A. Usié (CEECINST/00100/2021/CP2774/CT0001), and Research Contract to P. M. Barros (DL57/2016/CP1369/CT0029)pt_PT
dc.relation“FASTBREED: implementation of a breeding program on wheat varieties based on genomic selection” (ALT20-03-0145-FEDER-000018). We also thank FCT for the financial support to Research Units UIDB/05183/2020 (MED-Mediterranean Institute for Agriculture, Environment and Development) and GREEN-IT-Bioresources for Sustainability (UIDB/04551/2020, UIDP/04551/2020) as well as LS4FUTURE (LA/P/0087/2020) Associated Laboratory.pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleAn improved reference genome and first organelle genomes of Quercus suberpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.issue6pt_PT
oaire.citation.titleTree Genetics & Genomespt_PT
oaire.citation.volume19pt_PT
person.familyNameMatos
person.givenNameJosé
person.identifier0000000068588745
person.identifier.ciencia-id7C19-72D4-D3DF
person.identifier.orcid0000-0001-8772-6223
person.identifier.scopus-author-id56304302400
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication08be9319-6e65-44fa-acfb-ec10f2fc56c8
relation.isAuthorOfPublication.latestForDiscovery08be9319-6e65-44fa-acfb-ec10f2fc56c8

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