The draft genome sequence of cork oak

António Marcos Ramos, Ana Usié, Pedro Barbosa, Pedro M. Barros, Tiago Capote, Inês Chaves, Fernanda Simões, Isabel Abreu, Isabel Carrasquinho, Carlos Faro, Joana B. Guimarães, Diogo Mendonça, Filomena Nóbrega, Leandra Rodrigues, Nelson J.M. Saibo, Maria Carolina Varela, Conceição Egas, José Matos, Célia M. Miguel, M. Margarida Oliveira & 2 others Cândido P. Ricardo, Sónia Gonçalves

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.

Original languageEnglish
Article number180069
JournalScientific Data
Volume5
DOIs
Publication statusPublished - 22 May 2018

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Genome
Genes
High Throughput
Gene
confidence
Scaffold
Throughput
industry
Confidence
Annotation
Completeness
Assignment
Signature
Availability
community
Draft
Industry
Scaffolds
Dependent
Africa

Cite this

Ramos, A. M., Usié, A., Barbosa, P., Barros, P. M., Capote, T., Chaves, I., ... Gonçalves, S. (2018). The draft genome sequence of cork oak. Scientific Data, 5, [180069]. https://doi.org/10.1038/sdata.2018.69
Ramos, António Marcos ; Usié, Ana ; Barbosa, Pedro ; Barros, Pedro M. ; Capote, Tiago ; Chaves, Inês ; Simões, Fernanda ; Abreu, Isabel ; Carrasquinho, Isabel ; Faro, Carlos ; Guimarães, Joana B. ; Mendonça, Diogo ; Nóbrega, Filomena ; Rodrigues, Leandra ; Saibo, Nelson J.M. ; Varela, Maria Carolina ; Egas, Conceição ; Matos, José ; Miguel, Célia M. ; Oliveira, M. Margarida ; Ricardo, Cândido P. ; Gonçalves, Sónia. / The draft genome sequence of cork oak. In: Scientific Data. 2018 ; Vol. 5.
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Ramos, AM, Usié, A, Barbosa, P, Barros, PM, Capote, T, Chaves, I, Simões, F, Abreu, I, Carrasquinho, I, Faro, C, Guimarães, JB, Mendonça, D, Nóbrega, F, Rodrigues, L, Saibo, NJM, Varela, MC, Egas, C, Matos, J, Miguel, CM, Oliveira, MM, Ricardo, CP & Gonçalves, S 2018, 'The draft genome sequence of cork oak', Scientific Data, vol. 5, 180069. https://doi.org/10.1038/sdata.2018.69

The draft genome sequence of cork oak. / Ramos, António Marcos; Usié, Ana; Barbosa, Pedro; Barros, Pedro M.; Capote, Tiago; Chaves, Inês; Simões, Fernanda; Abreu, Isabel; Carrasquinho, Isabel; Faro, Carlos; Guimarães, Joana B.; Mendonça, Diogo; Nóbrega, Filomena; Rodrigues, Leandra; Saibo, Nelson J.M.; Varela, Maria Carolina; Egas, Conceição; Matos, José; Miguel, Célia M.; Oliveira, M. Margarida; Ricardo, Cândido P.; Gonçalves, Sónia.

In: Scientific Data, Vol. 5, 180069, 22.05.2018.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The draft genome sequence of cork oak

AU - Ramos, António Marcos

AU - Usié, Ana

AU - Barbosa, Pedro

AU - Barros, Pedro M.

AU - Capote, Tiago

AU - Chaves, Inês

AU - Simões, Fernanda

AU - Abreu, Isabel

AU - Carrasquinho, Isabel

AU - Faro, Carlos

AU - Guimarães, Joana B.

AU - Mendonça, Diogo

AU - Nóbrega, Filomena

AU - Rodrigues, Leandra

AU - Saibo, Nelson J.M.

AU - Varela, Maria Carolina

AU - Egas, Conceição

AU - Matos, José

AU - Miguel, Célia M.

AU - Oliveira, M. Margarida

AU - Ricardo, Cândido P.

AU - Gonçalves, Sónia

PY - 2018/5/22

Y1 - 2018/5/22

N2 - Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.

AB - Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.

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JO - Scientific Data

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Ramos AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I et al. The draft genome sequence of cork oak. Scientific Data. 2018 May 22;5. 180069. https://doi.org/10.1038/sdata.2018.69