Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana

Autores
Pombo, Marina Alejandra; Ramos, Romina Nahir; Zheng, Yi; Fei, Zhangjun; Martin, Gregory B.; Rosli, Hernan Guillermo
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
RT-qPCR is a widely used technique for the analysis of gene expression. Accurate estimation of transcript abundance relies strongly on a normalization that requires the use of reference genes that are stably expressed in the conditions analyzed. Initially, they were adopted from those used in Northern blot experiments, but an increasing number of publications highlight the need to fnd and validate alternative reference genes for the particular system under study. The development of high-throughput sequencing techniques has facilitated the identifcation of such stably expressed genes. Nicotiana benthamiana has been extensively used as a model in the plant research feld. In spite of this, there is scarce information regarding suitable RT-qPCR reference genes for this species. Employing RNA-seq data previously generated from tomato plants, combined with newly generated data from N. benthamiana leaves infltrated with Pseudomonas fuorescens, we identifed and tested a set of 9 candidate reference genes. Using three diferent algorithms, we found that NbUbe35, NbNQO and NbErpA exhibit less variable gene expression in our pathosystem than previously used genes. Furthermore, the combined use of the frst two is sufcient for robust gene expression analysis. We encourage employing these novel reference genes in future RT-qPCR experiments involving N. benthamiana and Pseudomonas spp.
Fil: Pombo, Marina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Fil: Ramos, Romina Nahir. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Fil: Zheng, Yi. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Fei, Zhangjun. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Martin, Gregory B.. Boyce Thompson Institute for Plant Research; Estados Unidos. Cornell University; Estados Unidos
Fil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Materia
RT-qPCR
REFERENCE GENES
PLANT-BACTERIA INTERACTION
NICOTIANA BENTHAMIANA
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/152225
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamianaPombo, Marina AlejandraRamos, Romina NahirZheng, YiFei, ZhangjunMartin, Gregory B.Rosli, Hernan GuillermoRT-qPCRREFERENCE GENESPLANT-BACTERIA INTERACTIONNICOTIANA BENTHAMIANAhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1RT-qPCR is a widely used technique for the analysis of gene expression. Accurate estimation of transcript abundance relies strongly on a normalization that requires the use of reference genes that are stably expressed in the conditions analyzed. Initially, they were adopted from those used in Northern blot experiments, but an increasing number of publications highlight the need to fnd and validate alternative reference genes for the particular system under study. The development of high-throughput sequencing techniques has facilitated the identifcation of such stably expressed genes. Nicotiana benthamiana has been extensively used as a model in the plant research feld. In spite of this, there is scarce information regarding suitable RT-qPCR reference genes for this species. Employing RNA-seq data previously generated from tomato plants, combined with newly generated data from N. benthamiana leaves infltrated with Pseudomonas fuorescens, we identifed and tested a set of 9 candidate reference genes. Using three diferent algorithms, we found that NbUbe35, NbNQO and NbErpA exhibit less variable gene expression in our pathosystem than previously used genes. Furthermore, the combined use of the frst two is sufcient for robust gene expression analysis. We encourage employing these novel reference genes in future RT-qPCR experiments involving N. benthamiana and Pseudomonas spp.Fil: Pombo, Marina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaFil: Ramos, Romina Nahir. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaFil: Zheng, Yi. Boyce Thompson Institute for Plant Research; Estados UnidosFil: Fei, Zhangjun. Boyce Thompson Institute for Plant Research; Estados UnidosFil: Martin, Gregory B.. Boyce Thompson Institute for Plant Research; Estados Unidos. Cornell University; Estados UnidosFil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaNature Publishing Group2019-02-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/152225Pombo, Marina Alejandra; Ramos, Romina Nahir; Zheng, Yi; Fei, Zhangjun; Martin, Gregory B.; et al.; Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana; Nature Publishing Group; Scientific Reports; 9; 1; 07-2-2019; 1-102045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-018-38247-2info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-018-38247-2info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:48:01Zoai:ri.conicet.gov.ar:11336/152225instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:48:01.524CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
title Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
spellingShingle Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
Pombo, Marina Alejandra
RT-qPCR
REFERENCE GENES
PLANT-BACTERIA INTERACTION
NICOTIANA BENTHAMIANA
title_short Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
title_full Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
title_fullStr Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
title_full_unstemmed Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
title_sort Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana
dc.creator.none.fl_str_mv Pombo, Marina Alejandra
Ramos, Romina Nahir
Zheng, Yi
Fei, Zhangjun
Martin, Gregory B.
Rosli, Hernan Guillermo
author Pombo, Marina Alejandra
author_facet Pombo, Marina Alejandra
Ramos, Romina Nahir
Zheng, Yi
Fei, Zhangjun
Martin, Gregory B.
Rosli, Hernan Guillermo
author_role author
author2 Ramos, Romina Nahir
Zheng, Yi
Fei, Zhangjun
Martin, Gregory B.
Rosli, Hernan Guillermo
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv RT-qPCR
REFERENCE GENES
PLANT-BACTERIA INTERACTION
NICOTIANA BENTHAMIANA
topic RT-qPCR
REFERENCE GENES
PLANT-BACTERIA INTERACTION
NICOTIANA BENTHAMIANA
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv RT-qPCR is a widely used technique for the analysis of gene expression. Accurate estimation of transcript abundance relies strongly on a normalization that requires the use of reference genes that are stably expressed in the conditions analyzed. Initially, they were adopted from those used in Northern blot experiments, but an increasing number of publications highlight the need to fnd and validate alternative reference genes for the particular system under study. The development of high-throughput sequencing techniques has facilitated the identifcation of such stably expressed genes. Nicotiana benthamiana has been extensively used as a model in the plant research feld. In spite of this, there is scarce information regarding suitable RT-qPCR reference genes for this species. Employing RNA-seq data previously generated from tomato plants, combined with newly generated data from N. benthamiana leaves infltrated with Pseudomonas fuorescens, we identifed and tested a set of 9 candidate reference genes. Using three diferent algorithms, we found that NbUbe35, NbNQO and NbErpA exhibit less variable gene expression in our pathosystem than previously used genes. Furthermore, the combined use of the frst two is sufcient for robust gene expression analysis. We encourage employing these novel reference genes in future RT-qPCR experiments involving N. benthamiana and Pseudomonas spp.
Fil: Pombo, Marina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Fil: Ramos, Romina Nahir. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Fil: Zheng, Yi. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Fei, Zhangjun. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Martin, Gregory B.. Boyce Thompson Institute for Plant Research; Estados Unidos. Cornell University; Estados Unidos
Fil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
description RT-qPCR is a widely used technique for the analysis of gene expression. Accurate estimation of transcript abundance relies strongly on a normalization that requires the use of reference genes that are stably expressed in the conditions analyzed. Initially, they were adopted from those used in Northern blot experiments, but an increasing number of publications highlight the need to fnd and validate alternative reference genes for the particular system under study. The development of high-throughput sequencing techniques has facilitated the identifcation of such stably expressed genes. Nicotiana benthamiana has been extensively used as a model in the plant research feld. In spite of this, there is scarce information regarding suitable RT-qPCR reference genes for this species. Employing RNA-seq data previously generated from tomato plants, combined with newly generated data from N. benthamiana leaves infltrated with Pseudomonas fuorescens, we identifed and tested a set of 9 candidate reference genes. Using three diferent algorithms, we found that NbUbe35, NbNQO and NbErpA exhibit less variable gene expression in our pathosystem than previously used genes. Furthermore, the combined use of the frst two is sufcient for robust gene expression analysis. We encourage employing these novel reference genes in future RT-qPCR experiments involving N. benthamiana and Pseudomonas spp.
publishDate 2019
dc.date.none.fl_str_mv 2019-02-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/152225
Pombo, Marina Alejandra; Ramos, Romina Nahir; Zheng, Yi; Fei, Zhangjun; Martin, Gregory B.; et al.; Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana; Nature Publishing Group; Scientific Reports; 9; 1; 07-2-2019; 1-10
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/152225
identifier_str_mv Pombo, Marina Alejandra; Ramos, Romina Nahir; Zheng, Yi; Fei, Zhangjun; Martin, Gregory B.; et al.; Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana; Nature Publishing Group; Scientific Reports; 9; 1; 07-2-2019; 1-10
2045-2322
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-018-38247-2
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-018-38247-2
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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