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

Detalhes bibliográficos
Autor(a) principal: Pereira-Leal, José B.
Data de Publicação: 2014
Outros Autores: 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.
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.
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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
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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
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eu_rights_str_mv openAccess
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dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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