A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.1/4471 |
Resumo: | 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 http://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. |
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spelling |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencingBackground: 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 http://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.BioMed CentralSapientiaPereira-Leal, José B.Abreu, Isabel A.Alabaça, Cláudia S.Almeida, Maria H.Almeida, PauloAlmeida, TâniaAmorim, Maria I.Araújo, SusanaAzevedo, HerlânderBadia, AleixBatista, DoraBohn, AndreasCapote, TiagoCarrasquinho, IsabelChaves, InêsCoelho, A. C.Costa, Maria M. R.Costa, RitaCravador, A.Egas, ConceiçãoFaro, CarlosFortes, Ana M.Fortunato, Ana S.Gaspar, Maria J.Gonçalves, SóniaGraça, JoséHorta, MaríliaInácio, VeraLeitão, J. M.Lino-Neto, TeresaMarum, LilianaMatos, JoséMendonça, DiogoMiguel, AndreiaMiguel, Célia M.Morais-Cecílio, LeonorNeves, IsabelNóbrega, FilomenaOliveira, Maria M.Oliveira, RutePais, Maria S.Paiva, Jorge A.Paulo, O. S.Pinheiro, MiguelRaimundo, João A. P.Ramalho, J. C.Ribeiro, Ana I.Ribeiro, TeresaRocheta, MargaridaRodrigues, Ana I.Rodrigues, José C.Saibo, Nelson J. M.Santo, TatianaSantos, Ana M.Sá-Pereira, PaulaSebastiana, MónicaSimões, FernandaSobral, Rómulo S.Tavares, RuiTeixeira, RitaVarela, CarolinaVeloso, Maria M.Ricardo, Cândido P. P.2014-06-24T12:07:56Z2014-05-152014-06-18T11:04:14Z2014-05-15T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articletext/xmlapplication/pdfhttp://hdl.handle.net/10400.1/4471engBMC Genomics. 2014 May 15;15(1):371http://dx.doi.org/10.1186/1471-2164-15-371info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-24T10:15:49Zoai:sapientia.ualg.pt:10400.1/4471Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:57:53.735132Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
title |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
spellingShingle |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing Pereira-Leal, José B. |
title_short |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
title_full |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
title_fullStr |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
title_full_unstemmed |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
title_sort |
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
author |
Pereira-Leal, José B. |
author_facet |
Pereira-Leal, José B. Abreu, Isabel A. Alabaça, Cláudia S. Almeida, Maria H. Almeida, Paulo Almeida, Tânia Amorim, Maria I. Araújo, Susana Azevedo, Herlânder Badia, Aleix Batista, Dora Bohn, Andreas Capote, Tiago Carrasquinho, Isabel Chaves, Inês Coelho, A. C. Costa, Maria M. R. Costa, Rita Cravador, A. Egas, Conceição Faro, Carlos Fortes, Ana M. Fortunato, Ana S. Gaspar, Maria J. Gonçalves, Sónia Graça, José Horta, Marília Inácio, Vera Leitão, J. M. Lino-Neto, Teresa Marum, Liliana Matos, José Mendonça, Diogo Miguel, Andreia Miguel, Célia M. Morais-Cecílio, Leonor Neves, Isabel Nóbrega, Filomena Oliveira, Maria M. Oliveira, Rute Pais, Maria S. Paiva, Jorge A. Paulo, O. S. Pinheiro, Miguel Raimundo, João A. P. Ramalho, J. C. Ribeiro, Ana I. Ribeiro, Teresa Rocheta, Margarida Rodrigues, Ana I. Rodrigues, José C. Saibo, Nelson J. M. Santo, Tatiana Santos, Ana M. Sá-Pereira, Paula Sebastiana, Mónica Simões, Fernanda Sobral, Rómulo S. Tavares, Rui Teixeira, Rita Varela, Carolina Veloso, Maria M. Ricardo, Cândido P. P. |
author_role |
author |
author2 |
Abreu, Isabel A. Alabaça, Cláudia S. Almeida, Maria H. Almeida, Paulo Almeida, Tânia Amorim, Maria I. Araújo, Susana Azevedo, Herlânder Badia, Aleix Batista, Dora Bohn, Andreas Capote, Tiago Carrasquinho, Isabel Chaves, Inês Coelho, A. C. Costa, Maria M. R. Costa, Rita Cravador, A. Egas, Conceição Faro, Carlos Fortes, Ana M. Fortunato, Ana S. Gaspar, Maria J. Gonçalves, Sónia Graça, José Horta, Marília Inácio, Vera Leitão, J. M. Lino-Neto, Teresa Marum, Liliana Matos, José Mendonça, Diogo Miguel, Andreia Miguel, Célia M. Morais-Cecílio, Leonor Neves, Isabel Nóbrega, Filomena Oliveira, Maria M. Oliveira, Rute Pais, Maria S. Paiva, Jorge A. Paulo, O. S. Pinheiro, Miguel Raimundo, João A. P. Ramalho, J. C. Ribeiro, Ana I. Ribeiro, Teresa Rocheta, Margarida Rodrigues, Ana I. Rodrigues, José C. Saibo, Nelson J. M. Santo, Tatiana Santos, Ana M. Sá-Pereira, Paula Sebastiana, Mónica Simões, Fernanda Sobral, Rómulo S. Tavares, Rui Teixeira, Rita Varela, Carolina Veloso, Maria M. Ricardo, Cândido P. P. |
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 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 |
Sapientia |
dc.contributor.author.fl_str_mv |
Pereira-Leal, José B. Abreu, Isabel A. Alabaça, Cláudia S. Almeida, Maria H. Almeida, Paulo Almeida, Tânia Amorim, Maria I. Araújo, Susana Azevedo, Herlânder Badia, Aleix Batista, Dora Bohn, Andreas Capote, Tiago Carrasquinho, Isabel Chaves, Inês Coelho, A. C. Costa, Maria M. R. Costa, Rita Cravador, A. Egas, Conceição Faro, Carlos Fortes, Ana M. Fortunato, Ana S. Gaspar, Maria J. Gonçalves, Sónia Graça, José Horta, Marília Inácio, Vera Leitão, J. M. Lino-Neto, Teresa Marum, Liliana Matos, José Mendonça, Diogo Miguel, Andreia Miguel, Célia M. Morais-Cecílio, Leonor Neves, Isabel Nóbrega, Filomena Oliveira, Maria M. Oliveira, Rute Pais, Maria S. Paiva, Jorge A. Paulo, O. S. Pinheiro, Miguel Raimundo, João A. P. Ramalho, J. C. Ribeiro, Ana I. Ribeiro, Teresa Rocheta, Margarida Rodrigues, Ana I. Rodrigues, José C. Saibo, Nelson J. M. Santo, Tatiana Santos, Ana M. Sá-Pereira, Paula Sebastiana, Mónica Simões, Fernanda Sobral, Rómulo S. Tavares, Rui Teixeira, Rita Varela, Carolina Veloso, Maria M. Ricardo, Cândido P. P. |
description |
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 http://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. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-06-24T12:07:56Z 2014-05-15 2014-06-18T11:04:14Z 2014-05-15T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.1/4471 |
url |
http://hdl.handle.net/10400.1/4471 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
BMC Genomics. 2014 May 15;15(1):371 http://dx.doi.org/10.1186/1471-2164-15-371 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
text/xml application/pdf |
dc.publisher.none.fl_str_mv |
BioMed Central |
publisher.none.fl_str_mv |
BioMed Central |
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reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799133193512681472 |