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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2012
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v7_n10_p_Fernandez http://hdl.handle.net/20.500.12110/paper_19326203_v7_n10_p_Fernandez |
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paper:paper_19326203_v7_n10_p_Fernandez2023-06-08T16:30:59Z Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray Fernández, Paula Virginia Soria, Marcelo Abel Rivarola, Maximo Lisandro Peluffo, Lucila Hopp, Horacio Esteban Heinz, Ruth Amelia article computer program contig mapping controlled study crop improvement DNA microarray expressed sequence tag gene expression genetic transcription genome analysis Helianthus annuus molecular probe nonhuman plant breeding plant genetics real time polymerase chain reaction senescence sequence analysis species cultivation validation study water deficit water stress Expressed Sequence Tags Gene Expression Regulation, Plant Helianthus Oligonucleotide Array Sequence Analysis Helianthus Helianthus annuus 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. © 2012 Fernandez et al. Fil:Fernandez, P. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Soria, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Rivarola, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Peluffo, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Hopp, E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Heinz, R.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2012 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v7_n10_p_Fernandez http://hdl.handle.net/20.500.12110/paper_19326203_v7_n10_p_Fernandez |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
article computer program contig mapping controlled study crop improvement DNA microarray expressed sequence tag gene expression genetic transcription genome analysis Helianthus annuus molecular probe nonhuman plant breeding plant genetics real time polymerase chain reaction senescence sequence analysis species cultivation validation study water deficit water stress Expressed Sequence Tags Gene Expression Regulation, Plant Helianthus Oligonucleotide Array Sequence Analysis Helianthus Helianthus annuus |
| spellingShingle |
article computer program contig mapping controlled study crop improvement DNA microarray expressed sequence tag gene expression genetic transcription genome analysis Helianthus annuus molecular probe nonhuman plant breeding plant genetics real time polymerase chain reaction senescence sequence analysis species cultivation validation study water deficit water stress Expressed Sequence Tags Gene Expression Regulation, Plant Helianthus Oligonucleotide Array Sequence Analysis Helianthus Helianthus annuus Fernández, Paula Virginia Soria, Marcelo Abel Rivarola, Maximo Lisandro Peluffo, Lucila Hopp, Horacio Esteban Heinz, Ruth Amelia Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray |
| topic_facet |
article computer program contig mapping controlled study crop improvement DNA microarray expressed sequence tag gene expression genetic transcription genome analysis Helianthus annuus molecular probe nonhuman plant breeding plant genetics real time polymerase chain reaction senescence sequence analysis species cultivation validation study water deficit water stress Expressed Sequence Tags Gene Expression Regulation, Plant Helianthus Oligonucleotide Array Sequence Analysis Helianthus Helianthus annuus |
| 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. © 2012 Fernandez et al. |
| author |
Fernández, Paula Virginia Soria, Marcelo Abel Rivarola, Maximo Lisandro Peluffo, Lucila Hopp, Horacio Esteban Heinz, Ruth Amelia |
| author_facet |
Fernández, Paula Virginia Soria, Marcelo Abel Rivarola, Maximo Lisandro Peluffo, Lucila Hopp, Horacio Esteban Heinz, Ruth Amelia |
| author_sort |
Fernández, Paula Virginia |
| 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 |
| publishDate |
2012 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v7_n10_p_Fernandez http://hdl.handle.net/20.500.12110/paper_19326203_v7_n10_p_Fernandez |
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