Artículo

Fernandez, P.; Soria, M.; Blesa, D.; DiRienzo, J.; Moschen, S.; Rivarola, M.; Clavijo, B.J.; Gonzalez, S.; Peluffo, L.; Príncipi, D.; Dosio, G.; Aguirrezabal, L.; García-García, F.; Conesa, A.; Hopp, E.; Dopazo, J.; Heinz, R.A.; Paniego, N. "Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray" (2012) PLoS ONE. 7(10)
Este artículo es de Acceso Abierto y puede ser descargado en su versión final desde nuestro repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

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.

Registro:

Documento: Artículo
Título:Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
Autor:Fernandez, P.; Soria, M.; Blesa, D.; DiRienzo, J.; Moschen, S.; Rivarola, M.; Clavijo, B.J.; Gonzalez, S.; Peluffo, L.; Príncipi, D.; Dosio, G.; Aguirrezabal, L.; García-García, F.; Conesa, A.; Hopp, E.; Dopazo, J.; Heinz, R.A.; Paniego, N.
Filiación:Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
Departament of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba,, Argentina
Laboratorio de Fisiología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
Facultad de Ingeniería, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
Functional Genomics Node, National Institute of Bioinformatics, Centro de Investigación Príncipe Felipe, Valencia, Spain
Palabras clave: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
Año:2012
Volumen:7
Número:10
DOI: http://dx.doi.org/10.1371/journal.pone.0045899
Título revista:PLoS ONE
Título revista abreviado:PLoS ONE
ISSN:19326203
PDF:https://bibliotecadigital.exactas.uba.ar/download/paper/paper_19326203_v7_n10_p_Fernandez.pdf
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v7_n10_p_Fernandez

Referencias:

  • Vick, B.A., Hu, J., Future Prospects (2010) Genetics, Genomics and Breeding of Sunflower, pp. 313-326. , In: Hu J, Seiler G, Kole C, editors, Enfield, NH: Science Publishers
  • Paniego, N., Heinz, R., Fernandez, P., Talia, P., Nishinakamasu, V., Sunflower (2007) Genome Mapping and Molecular Breeding in Plants, pp. 153-177. , In: Kole C, editor, Berlin Heidelberg: Springer-Verlag
  • Seiler, G.J., Jan, C.C., Basic information (2010) Genetics, Genomics, and Breeding of Sunflower, pp. 2-50. , In: Hu J, Seiler GJ, Kole C, editors, Enfield, NH.: Science Publishers
  • Jan, C.C., Seiler, G.J., Sunflower (2007) Genetic Resources, Chromosome Engineering, and Crop Improvement Oilseed Crops, pp. 103-165. , In: Singh RJ, editor, CRC Press
  • Kane, N.C., Gill, N., King, M.J., Bowers, J.E., Berges, H., Progress towards a reference genome for sunflower (2011) Botany, 89, pp. 429-437
  • Hewezi, T., Petitprez, M., Gentzbittel, L., Primary metabolic pathways and signal transduction in sunflower (Helianthus annuus L.): comparison of transcriptional profiling in leaves and immature embryos using cDNA microarrays (2006) Planta, 223, pp. 948-964
  • Alignan, M., Hewezi, T., Petitprez, M., Dechamp-Guillaume, G., Gentzbittel, L., A cDNA microarray approach to decipher sunflower (Helianthus annuus) responses to the necrotrophic fungus Phoma macdonaldii (2006) New Phytol, 170, pp. 523-536
  • Hewezi, T., Leger, M., El Kayal, W., Gentzbittel, L., Transcriptional profiling of sunflower plants growing under low temperatures reveals an extensive down-regulation of gene expression associated with chilling sensitivity (2006) J Exp Bot, 57, pp. 3109-3122
  • Roche, J., Hewezi, T., Bouniols, A., Gentzbittel, L., Transcriptional profiles of primary metabolism and signal transduction-related genes in response to water stress in field-grown sunflower genotypes using a thematic cDNA microarray (2007) Planta, , DOI: 10.1007/s00425-007-0508-0
  • Fernandez, P., Di Rienzo, J.A., Fernandez, L., Hopp, H., Paniego, N., Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis (2008) BMC Plant Biology, 8
  • Lai, Z., Gross, B.L., Zou, Y., Andrews, J., Rieseberg, L.H., Microarray analysis reveals differential gene expression in hybrid sunflower species (2006) Mol Ecol, 15, pp. 1213-1227
  • Lai, Z., Kane, N.C., Zou, Y., Rieseberg, L.H., Natural variation in gene expression between wild and weedy populations of Helianthus annuus (2008) Genetics, 179, pp. 1881-1890
  • Brouillette, L.C., Donovan, L.A., Nitrogen stress response of a hybrid species: a gene expression study (2011) Annals of Botany, 107, pp. 101-108
  • Larkin, J.E., Franc, B.C., Gavras, H., Sultana, R., Quackenbush, J., Independence and reproducibility across microarray platforms (2005) Nat Methods, 2, pp. 337-344
  • Nazar, N.R., Chen, P., Dean, D., Robb, J., DNA Chip Analysis in Diverse Organisms with Unsequenced Genomes (2010) Mol Biotechnol, 44, pp. 8-13
  • Ophir, R., Eshed, R., Harel-Beja, R., Tzuri, G., Portnoy, V., High-throughput marker discovery in melon using a self-designed oligo microarray (2010) BMC Genomics, 11, p. 269
  • Arabidopsis Oligonucleotide Microarrays, , http://www.ag.arizona.edu/microarray, Available, Accessed 2010 Aug 10
  • Edwards, K.D., Bombarely, A., Story, G.W., Allen, F., Mueller, L.A., TobEA: an atlas of tobacco gene expression from seed to senescence (2010) BMC Genomics, 11, p. 142
  • http://www.ricearray.org, NSF Rice Oligonucleotide Array Project. Available. Accessed 2010 Aug 10; http://www.maizearray.org, Maize Oligonucleotide Array Project. Available. Accessed 2010 Aug 10; Fenart, S., Assoumou, N.Y.-P., Duarte, J., Rivière, N., Wilmer, J., Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray (2010) BMC Genomics, 11
  • Martinez-Godoy, M.A., Mauri, N., Juarez, J., Carmen Marques, M., Santiago, J., A genome-wide 20 K citrus microarray for gene expression analysis (2008) BMC Genomics, 9
  • Mascarrell-Creus, A., Cañizares, J., Vilarrasa-Blasi, J., Mora-Garcia, S., Blanca, J., An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.) (2009) BMC Genomics, 10
  • Privat, I., Bardil, A., Gomez, A.B., Severac, D., Dantec, C., The 'PUCE CAFE' Project: the first 15 K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits (2011) BMC Genomics, 12, p. 5
  • Trick, M., Long, Y., Meng, J., Bancroft, I., Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing (2009) Plant Biotechnol J, 7, pp. 334-346
  • Udall, J.E., Flagel, L.E., Cheung, F., Woodward, A.W., Hovav, R., Spotted cotton oligonucleotide microarrays for gene expression analysis (2007) BMC Genomics, 8, p. 81
  • Wan, Y., Underwood, C., Toole, G., Skeggs, P., Zhu, T., A novel transcriptomic approach to identify candidate genes for grain quality traits in wheat (2009) Plant Biotechnol J, 7, pp. 401-410
  • Cheng, F., Liu, S., Wu, J., Fang, L., Sun, S., BRAD, the genetics and genomics database for Brassica plants (2011) BMC Plant Biology, 11, p. 136
  • http://ted.bti.cornell.edu/, Tomato Functional Genomics Database. Available. Accessed 2010 Aug 10; Lai, Z., Kane, N.C., Kozik, A., Hodgins, K.A., Dlugosch, K.M., Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression (2012) Am J Bot, 99, pp. 209-218
  • Bazin, J., Langlade, N., Vincourt, P., Arribat, S., Balzergue, S., Targeted mRNA oxidation regulates sunflower seed dormancy alleviation during dry after-ripening (2011) Plant Cell, 23, pp. 2196-2208
  • Bachlava, E., Taylor, C.A., Tang, S., Bowers, J.E., Mandel, J.R., SNP discovery and development of a high-density genotyping array for sunflower (2012) PLoS ONE, 7, pp. e29814
  • Hardiman, G., Microarray platforms-comparisons and contrasts (2004) Pharmacogenomics, 5, pp. 487-502
  • Huang, X., Madan, A., CAP3: A DNA sequence assembly program (1999) Genome Res, 9, pp. 868-877
  • Booman, M., Borza, T., Feng, C.Y., Hori, T.S., Higgins, B., Development and Experimental Validation of a 20 K Atlantic Cod (Gadus morhua) Oligonucleotide Microarray Based on a Collection of over 150,000 ESTs (2010) Mar Biotechnol, , DOI:10.1007/s10126-010-9335-6
  • Close, T.J., Wanamaker, S.I., Caldo, R.A., Turner, S.M., Ashlock, D.A., A New Resource for Cereal Genomics: 22 K Barley GeneChip Comes of Age (2004) Plant Physiology, 134, pp. 960-968
  • Trick, M., Cheung, F., Drou, N., Fraser, F., Lobenhofer, E.K., A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences (2009) BMC Plant Biology, 9
  • Ewing, R.M., Claverie, J.M., EST databases as multi-conditional gene expression datasets (2000) Pac Symp Biocomput, pp. 430-442
  • Audic, S., Claverie, J.M., The significance of digital gene expression profiles (1997) Genome Research, 7, pp. 986-995
  • http://atgc-sur.inta.gob.ar, Sunflower Unigene Resource (SUR v1.0). Available: Accessed 2012 Sept 29; Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research (2005) Bioinformatics, 21, pp. 3674-3676
  • Gotz, S., Garcia-Gomez, J.M., Terol, J., Williams, T.D., Nagaraj, S.H., High-throughput functional annotation and data mining with the Blast2GO suite (2008) Nucleic Acids Res, 36, pp. 3420-3435
  • Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., InterProScan: protein domains identifier (2005) Nucleic Acids Research, 33, pp. W116-W120
  • Novaes, E., Drost, D., Farmerie, W., Pappas, G., Grattapaglia, D., High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome (2008) BMC Genomics, 9, p. 312
  • Rabbani, M.A., Maruyama, K., Abe, H., Khan, M.A., Katsura, K., Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses (2003) Plant Physiol, 133, pp. 1755-1767
  • Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Minimum information about a microarray experiment (MIAME)-toward standards for microarray data (2001) Nat Genet, 29, pp. 365-371
  • Fernandez, P., Di Rienzo, J.A., Moschen, S., Dosio, G.A.A., Aguirrezabal, L.A.N., Comparison of predictive methods and biological validation for qPCR reference genes in sunflower leaf senescence transcript analysis (2011) Plant Cell Report, 30, pp. 63-74
  • Al-Shahrour, F., Arbiza, L., Dopazo, H., Huerta-Cepas, J., Minguez, P., From genes to functional classes in the study of biological systems (2007) BMC Bioinformatics, 8, p. 114
  • Smyth, G., Linear models and empirical bayes methods for assessing differential expression in microarray experiments (2004) Stat Appl Genet Mol Biol, 3, pp. Article3
  • Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nat Genet, 25, pp. 25-29
  • Al-Shahrour, F., Minguez, P., Vaquerizas, J.M., Conde, L., Dopazo, J., BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments (2005) Nucleic Acids Res, 33, pp. W460-W464
  • Pfaffl, M.W., A new mathematical model for relative quantification in real-time RT-PCR (2001) Nucleic Acid Research, 29, pp. e45. , 2001
  • Schena, M., Shalon, D., Davis, R.W., Brown, P.O., Quantitative monitoring of gene expression patterns with a complementary DNA microarray (1995) Science, 270, pp. 467-470
  • Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Accessing genetic information with high-density DNA arrays (1996) Science, 274, pp. 610-614
  • Chen, Y.A., Mckillen, D.J., Wu, S., Jenny, M.J., Chapman, R., Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information (2004) BMC Bioinformatics, 5
  • Clarke, J.D., Zhu, T., Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives (2006) Plant J, 45, pp. 630-650
  • Wurmbach, E., Yuen, T., Sealfon, S.C., Focused microarray analysis (2003) Methods, 31, pp. 306-316
  • Boguski, M.S., Lowe, T.M., Tolstoshev, C.M., dbEST-database for "expressed sequence tags" (1993) Nat Genet, 4, pp. 332-333
  • Rensink, W.A., Buell, R., Microarray expression profiling resources for plant genomics (2005) Trends in Plant Science, 10, pp. 1360-1385
  • Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles (2005) Proc Natl Acad Sci U S A, 102, pp. 15545-15550
  • Li, X., Chiang, H.-I., Zhu, J., Dowd, S.E., Zhou, H., Characterization of a newly developed chicken 44 K Agilent microarray (2008) BMC Genomics, 9, p. 60
  • Forment, J., Gadea, J., Huerta, L., Abizanda, J., Agusti, S., Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies (2005) Plant Molecular Biology, 57, pp. 375-391
  • Heesacker, A., Kishore, V.K., Gao, W., Tang, S., Kolkman, J.M., SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility (2008) Theor Appl Genet, 117, pp. 1021-1029
  • Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D., Basic local alignment search tool (1990) Journal of Molecular Biology, 215, pp. 403-410
  • Rice, P., Longden, I., Bleasby, A., EMBOSS: The European Molecular Biology Open Software Suite (2000) Trends in Genetics, 16, pp. 276-277
  • Bolstad, B.M., Irizarry, R.A., Astrand, M., Speed, T.P., A comparison of normalization methods for high density oligonucleotide array data based on variance and bias (2003) Bioinformatics, 19, pp. 185-193
  • Rozen, S., Skaletsky, H., (2000) Primer3 on the WWW for general users and for biologist programmers, pp. 365-386. , Krawetz S MSe, editor. Totowa, NJ: Humana Press
  • Ruijter, J., Ramakers, C., Hoogaars, W., Karlen, Y., Bakker, O., Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data (2009) Nucl Acids Res, 37, pp. e45
  • Di Rienzo, J.A., (2009) fgStatistics, , http://sitesgooglecom/site/fgstatistics, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Argentina. Available, Accessed 2012 Aug 27

Citas:

---------- APA ----------
Fernandez, P., Soria, M., Blesa, D., DiRienzo, J., Moschen, S., Rivarola, M., Clavijo, B.J.,..., Paniego, N. (2012) . Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray. PLoS ONE, 7(10).
http://dx.doi.org/10.1371/journal.pone.0045899
---------- CHICAGO ----------
Fernandez, P., Soria, M., Blesa, D., DiRienzo, J., Moschen, S., Rivarola, M., et al. "Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray" . PLoS ONE 7, no. 10 (2012).
http://dx.doi.org/10.1371/journal.pone.0045899
---------- MLA ----------
Fernandez, P., Soria, M., Blesa, D., DiRienzo, J., Moschen, S., Rivarola, M., et al. "Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray" . PLoS ONE, vol. 7, no. 10, 2012.
http://dx.doi.org/10.1371/journal.pone.0045899
---------- VANCOUVER ----------
Fernandez, P., Soria, M., Blesa, D., DiRienzo, J., Moschen, S., Rivarola, M., et al. Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray. PLoS ONE. 2012;7(10).
http://dx.doi.org/10.1371/journal.pone.0045899