Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles

Autores
Fay, Jessica Vannina; Watkins, Christopher J.; Shrestha, Ram K.; Litwiñiuk, Sergio Leandro; Talavera Stefani, Liliana Noelia; Rojas, Cristian A.; Argüelles, Carina Francisca; Ferreras, Julián Alberto; Cáccamo, Mario José; Miretti, Marcos Mateo
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Fil: Fay, Jessica Vannina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Fay, Jessica Vannina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Watkins, Christopher J. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido.
Fil: Watkins, Christopher J. Norwich Research Park. Earlham Institute; Reino Unido.
Fil: Shrestha, Ram K. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido.
Fil: Shrestha, Ram K. Norwich Research Park. Earlham Institute; Reino Unido.
Fil: Litwiñiuk, Sergio Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Litwiñiuk, Sergio Leandro. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Talavera Stefani, Liliana Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Talavera Stefani, Liliana Noelia. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Rojas, Cristian A. Universidad Federal de la Integración Latinoamericana; Brasil.
Fil: Argüelles, Carina Francisca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Argüelles, Carina Francisca. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Ferreras, Julian Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Ferreras, Julian Alberto. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Cáccamo, Mario José. Parque de investigación de Norwich. Centro de Análisis del Genoma; Reino Unido.
Fil: Cáccamo, Mario José. Instituto Nacional de Botánica Agropecuaria. Parque de investigación de Norwich; Reino Unido.
Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Miretti, Marcos Mateo. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Química y Naturales. Instituto de Biología Subtropical; Argentina.
Background: The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. Results: In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. Conclusions: Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves’ polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites.
Materia
Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
Nivel de accesibilidad
acceso abierto
Condiciones de uso
Atribución-NoComercial-CompartirIgual 4.0 Internacional
Repositorio
Repositorio Institucional Digital de la Universidad Nacional de Misiones (UNaM)
Institución
Universidad Nacional de Misiones
OAI Identificador
oai:rid.unam.edu.ar:20.500.12219/4325

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spelling Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profilesFay, Jessica VanninaWatkins, Christopher J.Shrestha, Ram K.Litwiñiuk, Sergio LeandroTalavera Stefani, Liliana NoeliaRojas, Cristian A.Argüelles, Carina FranciscaFerreras, Julián AlbertoCáccamo, Mario JoséMiretti, Marcos MateoIlex paraguariensisYerba mateTranscriptomeExpression profileFunctional annotationDe-novo assemblyPhenylpropanoidFil: Fay, Jessica Vannina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.Fil: Fay, Jessica Vannina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.Fil: Watkins, Christopher J. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido.Fil: Watkins, Christopher J. Norwich Research Park. Earlham Institute; Reino Unido.Fil: Shrestha, Ram K. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido.Fil: Shrestha, Ram K. Norwich Research Park. Earlham Institute; Reino Unido.Fil: Litwiñiuk, Sergio Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.Fil: Litwiñiuk, Sergio Leandro. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.Fil: Talavera Stefani, Liliana Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.Fil: Talavera Stefani, Liliana Noelia. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.Fil: Rojas, Cristian A. Universidad Federal de la Integración Latinoamericana; Brasil.Fil: Argüelles, Carina Francisca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.Fil: Argüelles, Carina Francisca. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.Fil: Ferreras, Julian Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.Fil: Ferreras, Julian Alberto. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.Fil: Cáccamo, Mario José. Parque de investigación de Norwich. Centro de Análisis del Genoma; Reino Unido.Fil: Cáccamo, Mario José. Instituto Nacional de Botánica Agropecuaria. Parque de investigación de Norwich; Reino Unido.Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.Fil: Miretti, Marcos Mateo. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Química y Naturales. Instituto de Biología Subtropical; Argentina.Background: The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. Results: In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. Conclusions: Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves’ polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites.BioMed Central2018-12-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdf2.639 MBhttps://hdl.handle.net/20.500.12219/4325enginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5240-6info:eu-repo/semantics/openAccessAtribución-NoComercial-CompartirIgual 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-sa/4.0/reponame:Repositorio Institucional Digital de la Universidad Nacional de Misiones (UNaM)instname:Universidad Nacional de Misiones2025-09-04T11:42:45Zoai:rid.unam.edu.ar:20.500.12219/4325instacron:UNAMInstitucionalhttps://rid.unam.edu.ar/Universidad públicahttps://www.unam.edu.ar/https://rid.unam.edu.ar/oai/rsnrdArgentinaopendoar:2025-09-04 11:42:45.747Repositorio Institucional Digital de la Universidad Nacional de Misiones (UNaM) - Universidad Nacional de Misionesfalse
dc.title.none.fl_str_mv Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
spellingShingle Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
Fay, Jessica Vannina
Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
title_short Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_full Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_fullStr Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_full_unstemmed Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_sort Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
dc.creator.none.fl_str_mv Fay, Jessica Vannina
Watkins, Christopher J.
Shrestha, Ram K.
Litwiñiuk, Sergio Leandro
Talavera Stefani, Liliana Noelia
Rojas, Cristian A.
Argüelles, Carina Francisca
Ferreras, Julián Alberto
Cáccamo, Mario José
Miretti, Marcos Mateo
author Fay, Jessica Vannina
author_facet Fay, Jessica Vannina
Watkins, Christopher J.
Shrestha, Ram K.
Litwiñiuk, Sergio Leandro
Talavera Stefani, Liliana Noelia
Rojas, Cristian A.
Argüelles, Carina Francisca
Ferreras, Julián Alberto
Cáccamo, Mario José
Miretti, Marcos Mateo
author_role author
author2 Watkins, Christopher J.
Shrestha, Ram K.
Litwiñiuk, Sergio Leandro
Talavera Stefani, Liliana Noelia
Rojas, Cristian A.
Argüelles, Carina Francisca
Ferreras, Julián Alberto
Cáccamo, Mario José
Miretti, Marcos Mateo
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
topic Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
dc.description.none.fl_txt_mv Fil: Fay, Jessica Vannina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Fay, Jessica Vannina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Watkins, Christopher J. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido.
Fil: Watkins, Christopher J. Norwich Research Park. Earlham Institute; Reino Unido.
Fil: Shrestha, Ram K. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido.
Fil: Shrestha, Ram K. Norwich Research Park. Earlham Institute; Reino Unido.
Fil: Litwiñiuk, Sergio Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Litwiñiuk, Sergio Leandro. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Talavera Stefani, Liliana Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Talavera Stefani, Liliana Noelia. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Rojas, Cristian A. Universidad Federal de la Integración Latinoamericana; Brasil.
Fil: Argüelles, Carina Francisca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Argüelles, Carina Francisca. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Ferreras, Julian Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Ferreras, Julian Alberto. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina.
Fil: Cáccamo, Mario José. Parque de investigación de Norwich. Centro de Análisis del Genoma; Reino Unido.
Fil: Cáccamo, Mario José. Instituto Nacional de Botánica Agropecuaria. Parque de investigación de Norwich; Reino Unido.
Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
Fil: Miretti, Marcos Mateo. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Química y Naturales. Instituto de Biología Subtropical; Argentina.
Background: The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. Results: In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. Conclusions: Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves’ polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites.
description Fil: Fay, Jessica Vannina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
publishDate 2018
dc.date.none.fl_str_mv 2018-12-07
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info:eu-repo/semantics/publishedVersion
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info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/20.500.12219/4325
url https://hdl.handle.net/20.500.12219/4325
dc.language.none.fl_str_mv eng
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Atribución-NoComercial-CompartirIgual 4.0 Internacional
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dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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