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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 unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST [greater than 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 less than 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.
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| Subjects: | 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, , |
| Online Access: | http://ceiba.agro.uba.ar/cgi-bin/koha/opac-detail.pl?biblionumber=46712 |
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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 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 |
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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 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 Fernández, Paula Soria, Marcelo Abel Blesa, David Di Rienzo, Julio Alejandro Moschen, Sebastián Rivarola, Máximo Clavijo, Bernardo José González, Sergio Peluffo, Lucila Príncipi, Dario Dosio, Guillermo Aníbal Adrián Aguirrezábal, Luis Adolfo Nazareno García García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma 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 [greater than 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 less than 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. |
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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 |
| author |
Fernández, Paula Soria, Marcelo Abel Blesa, David Di Rienzo, Julio Alejandro Moschen, Sebastián Rivarola, Máximo Clavijo, Bernardo José González, Sergio Peluffo, Lucila Príncipi, Dario Dosio, Guillermo Aníbal Adrián Aguirrezábal, Luis Adolfo Nazareno García García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma |
| author_facet |
Fernández, Paula Soria, Marcelo Abel Blesa, David Di Rienzo, Julio Alejandro Moschen, Sebastián Rivarola, Máximo Clavijo, Bernardo José González, Sergio Peluffo, Lucila Príncipi, Dario Dosio, Guillermo Aníbal Adrián Aguirrezábal, Luis Adolfo Nazareno García García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma |
| author_sort |
Fernández, Paula |
| 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 |
| url |
http://ceiba.agro.uba.ar/cgi-bin/koha/opac-detail.pl?biblionumber=46712 |
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1787218007559241728 |
| spelling |
KOHA-OAI-AGRO:467122023-11-23T14:52:04Zhttp://ceiba.agro.uba.ar/cgi-bin/koha/opac-detail.pl?biblionumber=46712AAGDevelopment, characterization and experimental validation of a cultivated sunflower [Helianthus annuus L.] gene expression oligonucleotide microarrayFernández, PaulaSoria, Marcelo AbelBlesa, DavidDi Rienzo, Julio AlejandroMoschen, SebastiánRivarola, MáximoClavijo, Bernardo JoséGonzález, SergioPeluffo, LucilaPríncipi, DarioDosio, Guillermo Aníbal AdriánAguirrezábal, Luis Adolfo NazarenoGarcía García, FranciscoConesa, AnaHopp, Horacio EstebanDopazo, JoaquínHeinz, Ruth AmeliaPaniego, Normatextengapplication/pdfOligonucleotide-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 [greater than 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 less than 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.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 [greater than 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 less than 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.COMPUTER PROGRAMCONTIG MAPPINGCONTROLLED STUDYCROP IMPROVEMENTDNA MICROARRAYEXPRESSED SEQUENCE TAGGENE EXPRESSIONGENETIC TRANSCRIPTIONGENOME ANALYSISHELIANTHUS ANNUUSMOLECULAR PROBENONHUMANPLANT BREEDINGPLANT GENETICSREAL TIME POLYMERASE CHAIN REACTIONSENESCENCESEQUENCE ANALYSISSPECIES CULTIVATIONVALIDATION STUDYWATER DEFICITWATER STRESSEXPRESSED SEQUENCE TAGSGENE EXPRESSION REGULATION, PLANTHELIANTHUSOLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSISPlos One |