Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification
Autor(a) principal: | |
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Data de Publicação: | 2017 |
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/10400.5/14458 |
Resumo: | Key message RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. Abstract The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development |
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Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specificationVitis vinifera ssp. sylvestrisRNA-seqDe novo assemblydifferential gene expressionsex lociKey message RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. Abstract The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud developmentSpringerRepositório da Universidade de LisboaRamos, Miguel Jesus NunesCoito, João LucasFino, JoanaCunha, JorgeSilva, HelenaAlmeida, Patrícia GomesCosta, Maria Manuela RibeiroAmâncio, SaraPaulo, Octávio S.Rocheta, Margarida2017-12-11T14:37:23Z2017-102017-10-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.5/14458engPlant Mol Biol (2017) 93:151–17010.1007/s11103-016-0553-9info: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:RCAAP2023-03-06T14:44:30Zoai:www.repository.utl.pt:10400.5/14458Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T17:00:16.882103Repositório 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 |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification |
title |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification |
spellingShingle |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification Ramos, Miguel Jesus Nunes Vitis vinifera ssp. sylvestris RNA-seq De novo assembly differential gene expression sex loci |
title_short |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification |
title_full |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification |
title_fullStr |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification |
title_full_unstemmed |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification |
title_sort |
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification |
author |
Ramos, Miguel Jesus Nunes |
author_facet |
Ramos, Miguel Jesus Nunes Coito, João Lucas Fino, Joana Cunha, Jorge Silva, Helena Almeida, Patrícia Gomes Costa, Maria Manuela Ribeiro Amâncio, Sara Paulo, Octávio S. Rocheta, Margarida |
author_role |
author |
author2 |
Coito, João Lucas Fino, Joana Cunha, Jorge Silva, Helena Almeida, Patrícia Gomes Costa, Maria Manuela Ribeiro Amâncio, Sara Paulo, Octávio S. Rocheta, Margarida |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
Ramos, Miguel Jesus Nunes Coito, João Lucas Fino, Joana Cunha, Jorge Silva, Helena Almeida, Patrícia Gomes Costa, Maria Manuela Ribeiro Amâncio, Sara Paulo, Octávio S. Rocheta, Margarida |
dc.subject.por.fl_str_mv |
Vitis vinifera ssp. sylvestris RNA-seq De novo assembly differential gene expression sex loci |
topic |
Vitis vinifera ssp. sylvestris RNA-seq De novo assembly differential gene expression sex loci |
description |
Key message RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. Abstract The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-12-11T14:37:23Z 2017-10 2017-10-01T00:00:00Z |
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/10400.5/14458 |
url |
http://hdl.handle.net/10400.5/14458 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Plant Mol Biol (2017) 93:151–170 10.1007/s11103-016-0553-9 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Springer |
publisher.none.fl_str_mv |
Springer |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
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 |
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1799131090600853504 |