Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits

Detalhes bibliográficos
Autor(a) principal: Yuyama, Priscila Mary
Data de Publicação: 2016
Outros Autores: Reis Júnior, Osvaldo, Ivamoto, Suzana Tiemi, Domingues, Douglas Silva [UNESP], Carazzolle, Marcelo Falsarella, Pereira, Gonçalo Amarante Guimarães, Charmetant, Pierre, Leroy, Thierry, Pereira, Luiz Filipe Protasio
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1007/s00438-015-1111-x
http://hdl.handle.net/11449/172472
Resumo: Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffeaeugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffeaarabica together with Coffeacanephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.
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spelling Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruitsCoffeaDifferentially expressed genesGene annotationHomeologousRNA-seqStudies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffeaeugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffeaarabica together with Coffeacanephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Programa de Pós-Graduação em Genética e Biologia Molecular Universidade Estadual de Londrina (UEL)Laboratório de Biotecnologia Vegetal Instituto Agronômico do Paraná (IAPAR)Laboratório de Genômica e Expressão Departamento de Genética Evolução e Bioagentes Instituto de Biologia Universidade Estadual de Campinas (UNICAMP), CampinasCentre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) UMR AGAP, 34398Embrapa CaféDepartment of Botany Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP)Department of Botany Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP)CNPq: 1002-02 PHEGECOUniversidade Estadual de Londrina (UEL)Instituto Agronômico do Paraná (IAPAR)Universidade Estadual de Campinas (UNICAMP)UMR AGAPEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade Estadual Paulista (Unesp)Yuyama, Priscila MaryReis Júnior, OsvaldoIvamoto, Suzana TiemiDomingues, Douglas Silva [UNESP]Carazzolle, Marcelo FalsarellaPereira, Gonçalo Amarante GuimarãesCharmetant, PierreLeroy, ThierryPereira, Luiz Filipe Protasio2018-12-11T17:00:33Z2018-12-11T17:00:33Z2016-02-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article323-336application/pdfhttp://dx.doi.org/10.1007/s00438-015-1111-xMolecular Genetics and Genomics, v. 291, n. 1, p. 323-336, 2016.1617-46231617-4615http://hdl.handle.net/11449/17247210.1007/s00438-015-1111-x2-s2.0-849556963762-s2.0-84955696376.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Genetics and Genomics1,1681,168info:eu-repo/semantics/openAccess2023-10-17T06:09:53Zoai:repositorio.unesp.br:11449/172472Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:12:10.561183Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
title Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
spellingShingle Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
Yuyama, Priscila Mary
Coffea
Differentially expressed genes
Gene annotation
Homeologous
RNA-seq
title_short Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
title_full Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
title_fullStr Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
title_full_unstemmed Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
title_sort Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
author Yuyama, Priscila Mary
author_facet Yuyama, Priscila Mary
Reis Júnior, Osvaldo
Ivamoto, Suzana Tiemi
Domingues, Douglas Silva [UNESP]
Carazzolle, Marcelo Falsarella
Pereira, Gonçalo Amarante Guimarães
Charmetant, Pierre
Leroy, Thierry
Pereira, Luiz Filipe Protasio
author_role author
author2 Reis Júnior, Osvaldo
Ivamoto, Suzana Tiemi
Domingues, Douglas Silva [UNESP]
Carazzolle, Marcelo Falsarella
Pereira, Gonçalo Amarante Guimarães
Charmetant, Pierre
Leroy, Thierry
Pereira, Luiz Filipe Protasio
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual de Londrina (UEL)
Instituto Agronômico do Paraná (IAPAR)
Universidade Estadual de Campinas (UNICAMP)
UMR AGAP
Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv Yuyama, Priscila Mary
Reis Júnior, Osvaldo
Ivamoto, Suzana Tiemi
Domingues, Douglas Silva [UNESP]
Carazzolle, Marcelo Falsarella
Pereira, Gonçalo Amarante Guimarães
Charmetant, Pierre
Leroy, Thierry
Pereira, Luiz Filipe Protasio
dc.subject.por.fl_str_mv Coffea
Differentially expressed genes
Gene annotation
Homeologous
RNA-seq
topic Coffea
Differentially expressed genes
Gene annotation
Homeologous
RNA-seq
description Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffeaeugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffeaarabica together with Coffeacanephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.
publishDate 2016
dc.date.none.fl_str_mv 2016-02-01
2018-12-11T17:00:33Z
2018-12-11T17:00:33Z
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://dx.doi.org/10.1007/s00438-015-1111-x
Molecular Genetics and Genomics, v. 291, n. 1, p. 323-336, 2016.
1617-4623
1617-4615
http://hdl.handle.net/11449/172472
10.1007/s00438-015-1111-x
2-s2.0-84955696376
2-s2.0-84955696376.pdf
url http://dx.doi.org/10.1007/s00438-015-1111-x
http://hdl.handle.net/11449/172472
identifier_str_mv Molecular Genetics and Genomics, v. 291, n. 1, p. 323-336, 2016.
1617-4623
1617-4615
10.1007/s00438-015-1111-x
2-s2.0-84955696376
2-s2.0-84955696376.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Molecular Genetics and Genomics
1,168
1,168
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 323-336
application/pdf
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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