Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray
Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower u...
| Autores principales: | , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
PLOS One
2020
|
| Materias: | |
| Acceso en línea: | https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0045899 http://hdl.handle.net/20.500.12123/8123 https://doi.org/10.1371/journal.pone.0045899 |
| _version_ | 1855484137744367616 |
|---|---|
| author | Fernandez, Paula Del Carmen Soria, Marcelo Abel Blesa, David Di Rienzo, Julio A. Moschen, Sebastian Nicolas Rivarola, Maximo Lisandro Clavijo, Bernardo Gonzalez, Sergio Peluffo, Lucila Principi, Dario Dosio, Guillermo Aguirrezabal, Luis García-García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma Beatriz |
| author_browse | Aguirrezabal, Luis Blesa, David Clavijo, Bernardo Conesa, Ana Di Rienzo, Julio A. Dopazo, Joaquín Dosio, Guillermo Fernandez, Paula Del Carmen García-García, Francisco Gonzalez, Sergio Heinz, Ruth Amelia Hopp, Horacio Esteban Moschen, Sebastian Nicolas Paniego, Norma Beatriz Peluffo, Lucila Principi, Dario Rivarola, Maximo Lisandro Soria, Marcelo Abel |
| author_facet | Fernandez, Paula Del Carmen Soria, Marcelo Abel Blesa, David Di Rienzo, Julio A. Moschen, Sebastian Nicolas Rivarola, Maximo Lisandro Clavijo, Bernardo Gonzalez, Sergio Peluffo, Lucila Principi, Dario Dosio, Guillermo Aguirrezabal, Luis García-García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma Beatriz |
| author_sort | Fernandez, Paula Del Carmen |
| collection | INTA Digital |
| description | Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01) allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement. |
| format | Artículo |
| id | INTA8123 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | PLOS One |
| publisherStr | PLOS One |
| record_format | dspace |
| spelling | INTA81232022-08-12T15:57:02Z Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray Fernandez, Paula Del Carmen Soria, Marcelo Abel Blesa, David Di Rienzo, Julio A. Moschen, Sebastian Nicolas Rivarola, Maximo Lisandro Clavijo, Bernardo Gonzalez, Sergio Peluffo, Lucila Principi, Dario Dosio, Guillermo Aguirrezabal, Luis García-García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma Beatriz Helianthus annuus Expresión Génica Genómica Transcripción Gene Expression Genomics Transcription Oligonucleotides Sunflower Oligonucleótidos Girasol Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01) allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement. Instituto de Biotecnología Fil: Fernandez, Paula Del Carmen. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía; Argentina Fil: Blesa, David. Centro de Investigación Príncipe Felipe. Departament of Bioinformatics and Genomics; España Fil: Di Rienzo, Julio A. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina Fil: Moschen, Sebastian Nicolas. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Clavijo, Bernardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Gonzalez, Sergio. Universidad de Buenos Aires. Facultad de Ingeniería; Argentina Fil: Peluffo, Lucila. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Principi, Dario. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Dosio, Guillermo Aníbal Adrián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: Aguirrezabal, Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: García-García, Francisco. Centro de Investigación Príncipe Felipe. Departament of Bioinformatics and Genomics; España Fil: Conesa, Ana. Centro de Investigación Príncipe Felipe. Departament of Bioinformatics and Genomics; España Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Dopazo, Joaquín. Centro de Investigación Príncipe Felipe. Computational Genomics Department; España Fil: Heinz, Ruth Amelia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina 2020-10-23T17:35:21Z 2020-10-23T17:35:21Z 2012-10 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0045899 http://hdl.handle.net/20.500.12123/8123 1932-6203 https://doi.org/10.1371/journal.pone.0045899 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf PLOS One PLoS ONE 7 (10) : e45899 (Octubre 2012) |
| spellingShingle | Helianthus annuus Expresión Génica Genómica Transcripción Gene Expression Genomics Transcription Oligonucleotides Sunflower Oligonucleótidos Girasol Fernandez, Paula Del Carmen Soria, Marcelo Abel Blesa, David Di Rienzo, Julio A. Moschen, Sebastian Nicolas Rivarola, Maximo Lisandro Clavijo, Bernardo Gonzalez, Sergio Peluffo, Lucila Principi, Dario Dosio, Guillermo Aguirrezabal, Luis García-García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma Beatriz Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray |
| title | Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray |
| title_full | Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray |
| title_fullStr | Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray |
| title_full_unstemmed | Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray |
| title_short | Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray |
| title_sort | development characterization and experimental validation of a cultivated sunflower helianthus annuus l gene expression oligonucleotide microarray |
| topic | Helianthus annuus Expresión Génica Genómica Transcripción Gene Expression Genomics Transcription Oligonucleotides Sunflower Oligonucleótidos Girasol |
| url | https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0045899 http://hdl.handle.net/20.500.12123/8123 https://doi.org/10.1371/journal.pone.0045899 |
| work_keys_str_mv | AT fernandezpauladelcarmen developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT soriamarceloabel developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT blesadavid developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT dirienzojulioa developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT moschensebastiannicolas developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT rivarolamaximolisandro developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT clavijobernardo developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT gonzalezsergio developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT peluffolucila developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT principidario developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT dosioguillermo developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT aguirrezaballuis developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT garciagarciafrancisco developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT conesaana developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT hopphoracioesteban developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT dopazojoaquin developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT heinzruthamelia developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray AT paniegonormabeatriz developmentcharacterizationandexperimentalvalidationofacultivatedsunflowerhelianthusannuuslgeneexpressionoligonucleotidemicroarray |