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...

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Autores principales:	Paula Fernandez, Marcelo Soria, David Blesa, Julio DiRienzo, Sebastian Moschen, Maximo Rivarola, Bernardo Jose Clavijo, Sergio Gonzalez, Lucila Peluffo, Dario Príncipi, Guillermo Dosio, Luis Aguirrezabal, Francisco García-García, Ana Conesa, Esteban Hopp, Joaquín Dopazo, Ruth Amelia Heinz, Norma Paniego
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/29ebfcda53064606a14b005f1fd884e1
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spelling	oai:doaj.org-article:29ebfcda53064606a14b005f1fd884e12021-11-18T08:10:55ZDevelopment, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.1932-620310.1371/journal.pone.0045899https://doaj.org/article/29ebfcda53064606a14b005f1fd884e12012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23110046/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Oligonucleotide-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.Paula FernandezMarcelo SoriaDavid BlesaJulio DiRienzoSebastian MoschenMaximo RivarolaBernardo Jose ClavijoSergio GonzalezLucila PeluffoDario PríncipiGuillermo DosioLuis AguirrezabalFrancisco García-GarcíaAna ConesaEsteban HoppJoaquín DopazoRuth Amelia HeinzNorma PaniegoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e45899 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Paula Fernandez Marcelo Soria David Blesa Julio DiRienzo Sebastian Moschen Maximo Rivarola Bernardo Jose Clavijo Sergio Gonzalez Lucila Peluffo Dario Príncipi Guillermo Dosio Luis Aguirrezabal Francisco García-García Ana Conesa Esteban Hopp Joaquín Dopazo Ruth Amelia Heinz Norma Paniego Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.
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	article
author	Paula Fernandez Marcelo Soria David Blesa Julio DiRienzo Sebastian Moschen Maximo Rivarola Bernardo Jose Clavijo Sergio Gonzalez Lucila Peluffo Dario Príncipi Guillermo Dosio Luis Aguirrezabal Francisco García-García Ana Conesa Esteban Hopp Joaquín Dopazo Ruth Amelia Heinz Norma Paniego
author_facet	Paula Fernandez Marcelo Soria David Blesa Julio DiRienzo Sebastian Moschen Maximo Rivarola Bernardo Jose Clavijo Sergio Gonzalez Lucila Peluffo Dario Príncipi Guillermo Dosio Luis Aguirrezabal Francisco García-García Ana Conesa Esteban Hopp Joaquín Dopazo Ruth Amelia Heinz Norma Paniego
author_sort	Paula Fernandez
title	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_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_sort	development, characterization and experimental validation of a cultivated sunflower (helianthus annuus l.) gene expression oligonucleotide microarray.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/29ebfcda53064606a14b005f1fd884e1
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Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

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