Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves.
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1129868 https://doi.org/10.1186/s12864-020-6518-z |
Resumo: | Background - Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing was used to compare contrasting P. notatum cytotypes to identify differential expression patterns and candidate genes involved in the regulation of expression of this trait. Results - We built a comprehensive transcriptome using leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids and a coexpression network based on pairwise correlations between transcript expression profiles. We identified genes exclusively expressed in each cytotype and genes differentially expressed between pairs of cytotypes. Gene Ontology enrichment analyses were performed to better interpret the data. We de novo assembled 114,306 reference transcripts. In total, 536 candidate genes possibly associated with apomixis were detected through statistical analyses of the differential expression data, and several interacting genes potentially linked to the apomixis-controlling region, genes that have already been reported in the literature, and their neighbors were transcriptionally related in the coexpression network. Conclusions - Apomixis is a highly desirable trait in modern agriculture due to the maintenance of the characteristics of the mother plant in the progeny. The reference transcriptome, candidate genes and their coexpression network identified in this work represent rich resources for future grass breeding programs. |
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Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves.Differential expressionGene coexpression networkRNA sequencingApomixisPaspalumBackground - Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing was used to compare contrasting P. notatum cytotypes to identify differential expression patterns and candidate genes involved in the regulation of expression of this trait. Results - We built a comprehensive transcriptome using leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids and a coexpression network based on pairwise correlations between transcript expression profiles. We identified genes exclusively expressed in each cytotype and genes differentially expressed between pairs of cytotypes. Gene Ontology enrichment analyses were performed to better interpret the data. We de novo assembled 114,306 reference transcripts. In total, 536 candidate genes possibly associated with apomixis were detected through statistical analyses of the differential expression data, and several interacting genes potentially linked to the apomixis-controlling region, genes that have already been reported in the literature, and their neighbors were transcriptionally related in the coexpression network. Conclusions - Apomixis is a highly desirable trait in modern agriculture due to the maintenance of the characteristics of the mother plant in the progeny. The reference transcriptome, candidate genes and their coexpression network identified in this work represent rich resources for future grass breeding programs.Fernanda A. de Oliveira, UNICAMP; BIANCA BACCILI ZANOTTO VIGNA, CPPSE; Carla C. da Silva, UNICAMP; ALESSANDRA PEREIRA FAVERO, CPPSE; FREDERICO DE PINA MATTA, CPPSE; ANA LUISA SOUSA AZEVEDO, CNPGL; Anete P. de Souza, UNICAMP.OLIVEIRA, F. A. deVIGNA, B. B. Z.SILVA, C. C. daFAVERO, A. P.MATTA, F. de P.AZEVEDO, A. L. S.SOUZA, A. P. de2024-02-06T11:33:46Z2024-02-06T11:33:46Z2021-02-082020info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleBMC Genomics, v. 21, article 78, 2020.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1129868https://doi.org/10.1186/s12864-020-6518-zenginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2024-02-06T11:33:46Zoai:www.alice.cnptia.embrapa.br:doc/1129868Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542024-02-06T11:33:46falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542024-02-06T11:33:46Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. |
title |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. |
spellingShingle |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. OLIVEIRA, F. A. de Differential expression Gene coexpression network RNA sequencing Apomixis Paspalum |
title_short |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. |
title_full |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. |
title_fullStr |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. |
title_full_unstemmed |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. |
title_sort |
Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves. |
author |
OLIVEIRA, F. A. de |
author_facet |
OLIVEIRA, F. A. de VIGNA, B. B. Z. SILVA, C. C. da FAVERO, A. P. MATTA, F. de P. AZEVEDO, A. L. S. SOUZA, A. P. de |
author_role |
author |
author2 |
VIGNA, B. B. Z. SILVA, C. C. da FAVERO, A. P. MATTA, F. de P. AZEVEDO, A. L. S. SOUZA, A. P. de |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Fernanda A. de Oliveira, UNICAMP; BIANCA BACCILI ZANOTTO VIGNA, CPPSE; Carla C. da Silva, UNICAMP; ALESSANDRA PEREIRA FAVERO, CPPSE; FREDERICO DE PINA MATTA, CPPSE; ANA LUISA SOUSA AZEVEDO, CNPGL; Anete P. de Souza, UNICAMP. |
dc.contributor.author.fl_str_mv |
OLIVEIRA, F. A. de VIGNA, B. B. Z. SILVA, C. C. da FAVERO, A. P. MATTA, F. de P. AZEVEDO, A. L. S. SOUZA, A. P. de |
dc.subject.por.fl_str_mv |
Differential expression Gene coexpression network RNA sequencing Apomixis Paspalum |
topic |
Differential expression Gene coexpression network RNA sequencing Apomixis Paspalum |
description |
Background - Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing was used to compare contrasting P. notatum cytotypes to identify differential expression patterns and candidate genes involved in the regulation of expression of this trait. Results - We built a comprehensive transcriptome using leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids and a coexpression network based on pairwise correlations between transcript expression profiles. We identified genes exclusively expressed in each cytotype and genes differentially expressed between pairs of cytotypes. Gene Ontology enrichment analyses were performed to better interpret the data. We de novo assembled 114,306 reference transcripts. In total, 536 candidate genes possibly associated with apomixis were detected through statistical analyses of the differential expression data, and several interacting genes potentially linked to the apomixis-controlling region, genes that have already been reported in the literature, and their neighbors were transcriptionally related in the coexpression network. Conclusions - Apomixis is a highly desirable trait in modern agriculture due to the maintenance of the characteristics of the mother plant in the progeny. The reference transcriptome, candidate genes and their coexpression network identified in this work represent rich resources for future grass breeding programs. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020 2021-02-08 2024-02-06T11:33:46Z 2024-02-06T11:33:46Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
BMC Genomics, v. 21, article 78, 2020. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1129868 https://doi.org/10.1186/s12864-020-6518-z |
identifier_str_mv |
BMC Genomics, v. 21, article 78, 2020. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1129868 https://doi.org/10.1186/s12864-020-6518-z |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
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Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
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EMBRAPA |
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EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
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1794503557510070272 |