Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , , , , , |
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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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 |
|
_version_ |
1808128479085985792 |