A comprehensive assessment of the transcriptome of Cork oak (Quercus suber) through EST sequencing

José B. Pereira-Leal; Isabel A. Abreu; Cláudia S. Alabaça; M. Helena Almeida; Paulo Almeida; Tânia Almeida; M. Isabel Amorim; Susana Araújo; Herlânder Azevedo; Aleix Badia; Dora Batista; Andreas Bohn; Tiago Capote; Isabel Carrasquinho; Inês Chaves; Ana Cristina Coelho; M. Manuela R. Costa; Rita Costa; Alfredo Cravador; Conceição Egas; Carlos Faro; A. Margarida Fortes; Ana S. Fortunato; Maria João Gaspar; Sónia Gonçalves; José Graça; Marília Horta; Vera Inácio; José M. Leitão; Teresa Lino-Neto; Liliana Marum; José Matos; Diogo Mendonça; Andreia Miguel; Célia M. Miguel; Leonor Morais-Cecílio; Isabel Neves; Filomena Nóbrega; M. Margarida Oliveira; Rute Oliveira; M. Salomé Pais; Jorge A.P. Paiva; Octávio S. Paulo; Miguel Pinheiro; João A.P. Raimundo; José C. Ramalho; Ana I. Ribeiro; Teresa Ribeiro; Margarida Rocheta; A. Isabel Rodrigues; José C. Rodrigues; Nelson J.M. Saibo; Tatiana E. Santo; A. Margarida Santos; Paula Sá-Pereira; Mónica Sebastiana; Fernanda Simões; Rómulo S. Sobral; Rui Tavares; Rita Teixeira; Carolina Varela; M. Manuela Veloso; Cândido P.P. Ricardo

doi:10.1186/1471-2164-15-371

A comprehensive assessment of the transcriptome of Cork oak (Quercus suber) through EST sequencing

José B. Pereira-Leal^*, Isabel A. Abreu, Cláudia S. Alabaça, M. Helena Almeida, Paulo Almeida, Tânia Almeida, M. Isabel Amorim, Susana Araújo, Herlânder Azevedo, Aleix Badia, Dora Batista, Andreas Bohn, Tiago Capote, Isabel Carrasquinho, Inês Chaves, Ana Cristina Coelho, M. Manuela R. Costa, Rita Costa, Alfredo Cravador, Conceição EgasCarlos Faro, A. Margarida Fortes, Ana S. Fortunato, Maria João Gaspar, Sónia Gonçalves, José Graça, Marília Horta, Vera Inácio, José M. Leitão, Teresa Lino-Neto, Liliana Marum, José Matos, Diogo Mendonça, Andreia Miguel, Célia M. Miguel, Leonor Morais-Cecílio, Isabel Neves, Filomena Nóbrega, M. Margarida Oliveira, Rute Oliveira, M. Salomé Pais, Jorge A.P. Paiva, Octávio S. Paulo, Miguel Pinheiro, João A.P. Raimundo, José C. Ramalho, Ana I. Ribeiro, Teresa Ribeiro, Margarida Rocheta, A. Isabel Rodrigues, José C. Rodrigues, Nelson J.M. Saibo, Tatiana E. Santo, A. Margarida Santos, Paula Sá-Pereira, Mónica Sebastiana, Fernanda Simões, Rómulo S. Sobral, Rui Tavares, Rita Teixeira, Carolina Varela, M. Manuela Veloso, Cândido P.P. Ricardo

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

35 Citations (Scopus)

Abstract

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

Original language	English
Article number	371
Journal	BMC Genomics
Volume	15
Issue number	1
DOIs	https://doi.org/10.1186/1471-2164-15-371 https://doi.org/10.1186/1471-2164-15-371
Publication status	Published - 15 May 2014
Externally published	Yes

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Pereira-Leal, J. B., Abreu, I. A., Alabaça, C. S., Almeida, M. H., Almeida, P., Almeida, T., Amorim, M. I., Araújo, S., Azevedo, H., Badia, A., Batista, D., Bohn, A., Capote, T., Carrasquinho, I., Chaves, I., Coelho, A. C., Costa, M. M. R., Costa, R., Cravador, A., ... Ricardo, C. P. P. (2014). A comprehensive assessment of the transcriptome of Cork oak (Quercus suber) through EST sequencing. BMC Genomics, 15(1), Article 371. https://doi.org/10.1186/1471-2164-15-371, https://doi.org/10.1186/1471-2164-15-371

@article{5537a1f44e434a1786d544256aef10d6,

title = "A comprehensive assessment of the transcriptome of Cork oak (Quercus suber) through EST sequencing",

abstract = "Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.",

author = "Pereira-Leal, {Jos{\'e} B.} and Abreu, {Isabel A.} and Alaba{\c c}a, {Cl{\'a}udia S.} and Almeida, {M. Helena} and Paulo Almeida and T{\^a}nia Almeida and Amorim, {M. Isabel} and Susana Ara{\'u}jo and Herl{\^a}nder Azevedo and Aleix Badia and Dora Batista and Andreas Bohn and Tiago Capote and Isabel Carrasquinho and In{\^e}s Chaves and Coelho, {Ana Cristina} and Costa, {M. Manuela R.} and Rita Costa and Alfredo Cravador and Concei{\c c}{\~a}o Egas and Carlos Faro and Fortes, {A. Margarida} and Fortunato, {Ana S.} and Gaspar, {Maria Jo{\~a}o} and S{\'o}nia Gon{\c c}alves and Jos{\'e} Gra{\c c}a and Mar{\'i}lia Horta and Vera In{\'a}cio and Leit{\~a}o, {Jos{\'e} M.} and Teresa Lino-Neto and Liliana Marum and Jos{\'e} Matos and Diogo Mendon{\c c}a and Andreia Miguel and Miguel, {C{\'e}lia M.} and Leonor Morais-Cec{\'i}lio and Isabel Neves and Filomena N{\'o}brega and Oliveira, {M. Margarida} and Rute Oliveira and Pais, {M. Salom{\'e}} and Paiva, {Jorge A.P.} and Paulo, {Oct{\'a}vio S.} and Miguel Pinheiro and Raimundo, {Jo{\~a}o A.P.} and Ramalho, {Jos{\'e} C.} and Ribeiro, {Ana I.} and Teresa Ribeiro and Margarida Rocheta and Rodrigues, {A. Isabel} and Rodrigues, {Jos{\'e} C.} and Saibo, {Nelson J.M.} and Santo, {Tatiana E.} and Santos, {A. Margarida} and Paula S{\'a}-Pereira and M{\'o}nica Sebastiana and Fernanda Sim{\~o}es and Sobral, {R{\'o}mulo S.} and Rui Tavares and Rita Teixeira and Carolina Varela and Veloso, {M. Manuela} and Ricardo, {C{\^a}ndido P.P.}",

year = "2014",

month = may,

day = "15",

doi = "10.1186/1471-2164-15-371",

language = "English",

volume = "15",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central Ltd.",

number = "1",

}

Pereira-Leal, JB, Abreu, IA, Alabaça, CS, Almeida, MH, Almeida, P, Almeida, T, Amorim, MI, Araújo, S, Azevedo, H, Badia, A, Batista, D, Bohn, A, Capote, T, Carrasquinho, I, Chaves, I, Coelho, AC, Costa, MMR, Costa, R, Cravador, A, Egas, C, Faro, C, Fortes, AM, Fortunato, AS, Gaspar, MJ, Gonçalves, S, Graça, J, Horta, M, Inácio, V, Leitão, JM, Lino-Neto, T, Marum, L, Matos, J, Mendonça, D, Miguel, A, Miguel, CM, Morais-Cecílio, L, Neves, I, Nóbrega, F, Oliveira, MM, Oliveira, R, Pais, MS, Paiva, JAP, Paulo, OS, Pinheiro, M, Raimundo, JAP, Ramalho, JC, Ribeiro, AI, Ribeiro, T, Rocheta, M, Rodrigues, AI, Rodrigues, JC, Saibo, NJM, Santo, TE, Santos, AM, Sá-Pereira, P, Sebastiana, M, Simões, F, Sobral, RS, Tavares, R, Teixeira, R, Varela, C, Veloso, MM & Ricardo, CPP 2014, 'A comprehensive assessment of the transcriptome of Cork oak (Quercus suber) through EST sequencing', BMC Genomics, vol. 15, no. 1, 371. https://doi.org/10.1186/1471-2164-15-371, https://doi.org/10.1186/1471-2164-15-371

TY - JOUR

T1 - A comprehensive assessment of the transcriptome of Cork oak (Quercus suber) through EST sequencing

AU - Pereira-Leal, José B.

AU - Abreu, Isabel A.

AU - Alabaça, Cláudia S.

AU - Almeida, M. Helena

AU - Almeida, Paulo

AU - Almeida, Tânia

AU - Amorim, M. Isabel

AU - Araújo, Susana

AU - Azevedo, Herlânder

AU - Badia, Aleix

AU - Batista, Dora

AU - Bohn, Andreas

AU - Capote, Tiago

AU - Carrasquinho, Isabel

AU - Chaves, Inês

AU - Coelho, Ana Cristina

AU - Costa, M. Manuela R.

AU - Costa, Rita

AU - Cravador, Alfredo

AU - Egas, Conceição

AU - Faro, Carlos

AU - Fortes, A. Margarida

AU - Fortunato, Ana S.

AU - Gaspar, Maria João

AU - Gonçalves, Sónia

AU - Graça, José

AU - Horta, Marília

AU - Inácio, Vera

AU - Leitão, José M.

AU - Lino-Neto, Teresa

AU - Marum, Liliana

AU - Matos, José

AU - Mendonça, Diogo

AU - Miguel, Andreia

AU - Miguel, Célia M.

AU - Morais-Cecílio, Leonor

AU - Neves, Isabel

AU - Nóbrega, Filomena

AU - Oliveira, M. Margarida

AU - Oliveira, Rute

AU - Pais, M. Salomé

AU - Paiva, Jorge A.P.

AU - Paulo, Octávio S.

AU - Pinheiro, Miguel

AU - Raimundo, João A.P.

AU - Ramalho, José C.

AU - Ribeiro, Ana I.

AU - Ribeiro, Teresa

AU - Rocheta, Margarida

AU - Rodrigues, A. Isabel

AU - Rodrigues, José C.

AU - Saibo, Nelson J.M.

AU - Santo, Tatiana E.

AU - Santos, A. Margarida

AU - Sá-Pereira, Paula

AU - Sebastiana, Mónica

AU - Simões, Fernanda

AU - Sobral, Rómulo S.

AU - Tavares, Rui

AU - Teixeira, Rita

AU - Varela, Carolina

AU - Veloso, M. Manuela

AU - Ricardo, Cândido P.P.

PY - 2014/5/15

Y1 - 2014/5/15

N2 - Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

AB - Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

UR - http://www.scopus.com/inward/record.url?scp=84901651648&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-15-371

DO - 10.1186/1471-2164-15-371

M3 - Article

C2 - 24885229

SN - 1471-2164

VL - 15

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 371

ER -

A comprehensive assessment of the transcriptome of Cork oak (Quercus suber) through EST sequencing

Abstract

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