Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem

Autores
Pombo, Marina Alejandra; Zheng, Yi; Fei, Zhangjun; Martin, Gregory; Rosli, Hernan Guillermo
Año de publicación
2025
Idioma
inglés
Tipo de recurso
conjunto de datos
Estado
Descripción
The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in di erent systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identi cation of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves in ltrated with di erent immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Speci cally, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT- qPCR experiments involving this pathosystem.
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: Zheng, Yi. Cornell University; Estados Unidos
Fil: Fei, Zhangjun. Cornell University; Estados Unidos
Fil: Martin, Gregory. 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
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/251823
Acceder
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spelling Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystemPombo, Marina AlejandraZheng, YiFei, ZhangjunMartin, GregoryRosli, Hernan Guillermohttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in di erent systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identi cation of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves in ltrated with di erent immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Speci cally, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT- qPCR experiments involving this pathosystem.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: Zheng, Yi. Cornell University; Estados UnidosFil: Fei, Zhangjun. Cornell University; Estados UnidosFil: Martin, Gregory. 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; Argentina2025info:ar-repo/semantics/conjuntoDeDatosv1.0info:eu-repo/semantics/dataSetapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelapplication/vnd.ms-excelhttp://hdl.handle.net/11336/251823Pombo, Marina Alejandra; Zheng, Yi; Fei, Zhangjun; Martin, Gregory; Rosli, Hernan Guillermo; (2025): Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem. Consejo Nacional de Investigaciones Científicas y Técnicas. (dataset). http://hdl.handle.net/11336/251823CONICET DigitalCONICETenginfo:eu-repo/grantAgreement/Ministerio de Ciencia. Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica/PICT2014-1589info:eu-repo/grantAgreement/Consejo Nacional de Investigaciones Científicas y Técnicas/PICT2014-1589info:eu-repo/grantAgreement/Consejo Nacional de Investigaciones Científicas y Técnicas/PICT2014-1589info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:43:26Zoai:ri.conicet.gov.ar:11336/251823instacron: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 09:43:27.196CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
title Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
spellingShingle Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
Pombo, Marina Alejandra
title_short Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
title_full Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
title_fullStr Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
title_full_unstemmed Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
title_sort Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
dc.creator.none.fl_str_mv Pombo, Marina Alejandra
Zheng, Yi
Fei, Zhangjun
Martin, Gregory
Rosli, Hernan Guillermo
author Pombo, Marina Alejandra
author_facet Pombo, Marina Alejandra
Zheng, Yi
Fei, Zhangjun
Martin, Gregory
Rosli, Hernan Guillermo
author_role author
author2 Zheng, Yi
Fei, Zhangjun
Martin, Gregory
Rosli, Hernan Guillermo
author2_role author
author
author
author
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in di erent systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identi cation of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves in ltrated with di erent immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Speci cally, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT- qPCR experiments involving this pathosystem.
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: Zheng, Yi. Cornell University; Estados Unidos
Fil: Fei, Zhangjun. Cornell University; Estados Unidos
Fil: Martin, Gregory. 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 The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in di erent systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identi cation of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves in ltrated with di erent immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Speci cally, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT- qPCR experiments involving this pathosystem.
publishDate 2025
dc.date.none.fl_str_mv 2025
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dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/251823
Pombo, Marina Alejandra; Zheng, Yi; Fei, Zhangjun; Martin, Gregory; Rosli, Hernan Guillermo; (2025): Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem. Consejo Nacional de Investigaciones Científicas y Técnicas. (dataset). http://hdl.handle.net/11336/251823
CONICET Digital
CONICET
url http://hdl.handle.net/11336/251823
identifier_str_mv Pombo, Marina Alejandra; Zheng, Yi; Fei, Zhangjun; Martin, Gregory; Rosli, Hernan Guillermo; (2025): Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem. Consejo Nacional de Investigaciones Científicas y Técnicas. (dataset). http://hdl.handle.net/11336/251823
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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info:eu-repo/grantAgreement/Consejo Nacional de Investigaciones Científicas y Técnicas/PICT2014-1589
info:eu-repo/grantAgreement/Consejo Nacional de Investigaciones Científicas y Técnicas/PICT2014-1589
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