Advertisement

Plant Molecular Biology

, Volume 57, Issue 3, pp 375–391 | Cite as

Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies

  • J. Forment
  • J. Gadea
  • L. Huerta
  • L. Abizanda
  • J. Agusti
  • S. Alamar
  • E. Alos
  • F. Andres
  • R. Arribas
  • J. P. Beltran
  • A. Berbel
  • M. A. Blazquez
  • J. Brumos
  • L. A. Canas
  • M. Cercos
  • J. M. Colmenero-Flores
  • A. Conesa
  • B. Estables
  • M. Gandia
  • J. L. Garcia-Martinez
  • J. Gimeno
  • A. Gisbert
  • G. Gomez
  • L. Gonzalez-Candelas
  • A. Granell
  • J. Guerri
  • M. T. Lafuente
  • F. Madueno
  • J. F. Marcos
  • M. C. Marques
  • F. Martinez
  • M. A. Martinez-Godoy
  • S. Miralles
  • P. Moreno
  • L. Navarro
  • V. Pallas
  • M. A. Perez-Amador
  • J. Perez-Valle
  • C. Pons
  • I. Rodrigo
  • P. L. Rodriguez
  • C. Royo
  • R. Serrano
  • G. Soler
  • F. Tadeo
  • M. Talon
  • J. Terol
  • M. Trenor
  • L. Vaello
  • O. Vicente
  • Ch. Vidal
  • L. Zacarias
  • V. ConejeroEmail author
Article

Abstract

A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.

Keywords

bioinformatics citrus EST genomics microarray transcriptome 

Abbreviations

BLAST

Basic Local Alignment Search Tool

CFGP

Citrus Functional Genomics Project

CEVd

Citrus exocortis viroid

CTV

Citrus tristeza virus

CV

coefficient of variation

EC

enzyme classification

EST

expressed sequence tag

FAO

Food and Agriculture Organization

GO

Gene Ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

MIPS

Munich Information Center for Protein Sequences

NCBI

National Center for Biotechnology Information

TAIR

The Arabidopsis Information Resource

UTR

untranslated region

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abbott, A., Georgi, L., Yvergniaux, D., Wang, Y., Blenda, A., Reighard, G., Inigo, M., Sosinski, B. 2002Peach the model genome for RosaceaeActa Hort.575145155Google Scholar
  2. Adams, M.D., Soares, M.B., Kerlavage, A.R., Fields, C., Venter, J.C. 1993Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA libraryNat. Genet.4373380Google Scholar
  3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. 1990Basic Local Alignment Search ToolJ. Mol. Biol.215403410Google Scholar
  4. Barrett, H.C., Rhodes, A.M. 1976A numerical taxonomic study of the affinity relationships in cultivated Citrus and its close relativesSystematic Botany1105136Google Scholar
  5. Bausher, M., Shatters, R., Chaparro, J., Dang, P., Hunter, V., Niedz, R.. 2003An expressed sequence tag (EST) set from Citrus sinensis L. Osbeck whole seedlings and the implications of further perennial source investigationsPlant Sci.165415422Google Scholar
  6. Brenner, E.D., Stevenson, D.W., McCombie, R.W., Katari, M.S., Rudd, S.A., Mayer, K.F., Palenchar, P.M., Runko, S.J., Twigg, R.W., Dai, G., Martienssen, R.A., Benfey, P.N., Coruzzi, G.M. 2003Expressed sequence tag analysis in Cycas, the most primitive living seed plantGenome Biol.4R78Google Scholar
  7. Bugos, R.C., Chiang, V.L., Zhang, X.-H., Campbell, E.R., Podila, G.K., Campbell, W.H. 1995RNA isolation from plant tissues recalcitrant to extraction in guanidineBioTechniques19734737PubMedGoogle Scholar
  8. Church, G.M., Gilbert, W. 1984Genomic sequencingProc. Natl. Acad. Sci. USA8119911995Google Scholar
  9. Clark, M.S., Edwards, Y.J.K., Peterson, S., Clifton, S.W., Thompson, A.J., Sasaki, M., Suzuki, Y., Kikuchi, K., Watabe, S., Kawakami, K., Sugano, S., Elgar, G., Johnson, S.L. 2003Fugu ESTs: news resources for transcription analysis and genome annotationGenome Res.1327472753Google Scholar
  10. Emmanuel, E., Levy, A.A. 2002Tomato mutants as tools for functional genomicsCurr. Opin. Plant Biol.5112117Google Scholar
  11. Evertsz, E.M., Au-Young, J., Ruvolo, M.V., Lim, A.C., Reynolds, M.A. 2001Hybridization cross-reactivity within homologous gene families on glass cDNA microarraysBiotechniques3111821192Google Scholar
  12. Ewing, B., Green, P. 1998Base-calling of automated sequencer traces using Phred. II. Error probabilitiesGenome Res.8186194Google Scholar
  13. Ewing, B., Hillier, L., Wendl, M.C., Green, P. 1998Base-calling of automated sequencer traces using Phred. I. Accuracy assessmentGenome Res.8175185Google Scholar
  14. Girke, T., Todd, J., Ruuska, S., White, J., Benning, Ch., Ohlrogge, J. 2000Microarray analysis of developing Arabidopsis seedPlant Physiol.12415701581Google Scholar
  15. Gordon, D., Abajian, C., Green, P. 1998Consed: a graphical tool for sequence finishingGenome Res.8195202Google Scholar
  16. Horvath, D.P., Schaffer, R., West, M., Wisman, E. 2003Arabidopsis microarrays identify conserved and differentially expressed genes involved in shoot growth and development from distantly related plant speciesPlant J.34125134Google Scholar
  17. Kawai, J., Shinagawa, A., Shibata, K., Yoshino, M., Itoh, M., Ishii, Y., Arakawa, T., Hara, A., Fukunishi, Y., Konno, H.,  et al. 2001Functional annotation of a full-length mouse cDNA collectionNature409685690CrossRefPubMedGoogle Scholar
  18. Lawrence, C.J., Dong, Q., Polacco, M.L., Seigfred, T.E., Brendel, V. 2004MaizeGDB, the community database for maize genetics and genomicsNucl. Acids Res.32D393D397Google Scholar
  19. McKinney, E.C., Ali, N., Traut, A., Feldmann, K.A., Belostotsky, D.A., McDowell, J.M., Meagher, R.B. 1995Sequence-based identification of T-DNA insertion mutations in Arabidopsis: actin mutants act2-1 and act4-1Plant J.8613622Google Scholar
  20. Meyer, K., Leube, M.P., Grill, E. 1994A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thalianaScience26414521455PubMedGoogle Scholar
  21. Navarro, L., Pina, J.A., Juarez, J., Ballester-Olmos, J.F., Arregui, J.M., Ortega, C., Navarro, A, Duran-Vila, N., Guerri, J., Moreno, P., Cambra, M. and Zaragoza, S. 2002. The Citrus variety improvement program in Spain in the period 1975–2001. Proceedings of the 15th Conference of the International Organization for Citrus Virol, In: N. Duran-Vila, R.G. Milne and J.V. da Grača (Eds.), International Organization for Citrus Virology, Riverside, CA, pp. 306–316Google Scholar
  22. Poustka, A.J., Groth, D., Hennig, S., Thamm, S., Cameron, A., Beck, A., Reinhardt, R., Herwig, R., Panopoulou, G., Lehrach, H. 2003Generation, annotation, evolutionary analysis, and database integration of 20.000 unique sea urchin EST clustersGenome Res.1327362746Google Scholar
  23. Rise, M.L., Schalburg, K.R., Brown, G.D., Mawer, M.A., Devlin, R.H., Kuipers, N., Busby, M., Beetz-Sargent, M., Alberto, R., Gibbs, A.R., Hunt, P., Shukin, R., Zeznik, J.A., Nelson, C., Jones, S.R.M., Smailus, D.E., Jones, S.J.M., Schein, J.E., Marra, M.A., Butterfield, Y.S.N., Stott, J.M., Ng, S.H.S., Davidson, W.S., Koop, B.F. 2004Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristicsGenome Res.14478490Google Scholar
  24. Ruan, Y., Gilmore, J., Conner, T. 1998Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarraysPlant J.15821833Google Scholar
  25. Schaffer, R., Landgraf, J., Accerbi, M., Simon, V.V., Larson, M., Wisman, E. 2001Microarray analysis of diurnal and circadian-regulated genes in ArabidopsisPlant Cell13113123Google Scholar
  26. Schena, M., Shalon, D., Davis, R.W., Brown, P.O. 1995Quantitative monitoring of gene expression patterns with a complementary DNA microarrayScience270467470PubMedGoogle Scholar
  27. Shimada, T., Kita, M., Endo, T., Fujii, H., Ueda, T., Moriguchi, T., Omura, M. 2003Expressed sequence tags of ovary tissue cDNA library in Citrus unshiu MarcPlant Sci.165167168Google Scholar
  28. The Arabidopsis Genome Initiative (AGI)2000Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature408796815Google Scholar
  29. Tusher, G.T., Tibshirani, R., Chu, G. 2001Significance analysis of microarrays applied to the ionizing radiation responseProc. Natl. Acad. Sci. USA9851165121Google Scholar
  30. Vettore, A.L., da Silva, F.R., Kemper, E.L., Souza, G.M., da Silva, A.M., Ferro, M.I.T., Henrique-Silva, F., Giglioti, E.A., Lemos, M.V.F., Coutinho, L.L.,  et al. 2003Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcaneGenome Res.1327252735Google Scholar
  31. Whetten, R., Sun, Y.H., Zhang, Y., Sederoff, R. 2001Functional genomics and cell wall biosynthesis in loblolly pinePlant Mol. Biol.47275291Google Scholar
  32. White, J.A., Todd, J., Newman, T., Focks, N., Girke, T., Martinezde Ilarduya, O., Jaworski, J.G., Ohlrogge, J.B., Benning, , Ch.,  2000A new set of Arabidopsis expressed sequence tags from developing seedsThe metabolic pathway from carbohydrates to seed oil. Plant Physiol.12415821594Google Scholar
  33. Whitfield, Ch.W., Band, M.R., Bonaldo, M.F., Kumar, Ch.G., Liu, L., Pardinas, J.R., Robertson, H.M., Soares, M.B., Robinson, G.E. 2002Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey beeGenome Res.12555566Google Scholar
  34. Xue, Y., Li, J., Xu, Z. 2003Recent highlights of the China Rice Functional Genomics ProgramTrends Genet.19390394Google Scholar
  35. Yamamoto, K., Sasaki, T. 1997Large-scale EST sequencing in ricePlant Mol. Biol.35135144Google Scholar
  36. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., Speed, T.P. 2002Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variationNucleic Acids Res.30e15Google Scholar
  37. Yazaki, J., Kojima, K., Suzuki, K., Kishimoto, N., Kikuchi, S. 2004The Rice PIPELINE: a unification tool for plant functional genomicsNucleic Acids Res.32D383D387Google Scholar
  38. Yue, H., Eastman, P.S., Wang, B.B., Minor, J., Doctolero, M.H., Nuttall, R.L., Stack, R., Becker, J.W., Montgomery, J.R., Vainer, M., Johnston, R. 2001An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expressionNucleic Acids Res.29e41Google Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • J. Forment
    • 1
  • J. Gadea
    • 1
  • L. Huerta
    • 1
  • L. Abizanda
    • 1
  • J. Agusti
    • 2
  • S. Alamar
    • 3
  • E. Alos
    • 2
  • F. Andres
    • 2
  • R. Arribas
    • 1
  • J. P. Beltran
    • 1
  • A. Berbel
    • 1
  • M. A. Blazquez
    • 1
  • J. Brumos
    • 2
  • L. A. Canas
    • 1
  • M. Cercos
    • 2
  • J. M. Colmenero-Flores
    • 2
  • A. Conesa
    • 2
  • B. Estables
    • 3
  • M. Gandia
    • 2
  • J. L. Garcia-Martinez
    • 1
  • J. Gimeno
    • 1
  • A. Gisbert
    • 1
  • G. Gomez
    • 1
  • L. Gonzalez-Candelas
    • 3
  • A. Granell
    • 1
  • J. Guerri
    • 2
  • M. T. Lafuente
    • 3
  • F. Madueno
    • 1
  • J. F. Marcos
    • 3
  • M. C. Marques
    • 1
  • F. Martinez
    • 2
  • M. A. Martinez-Godoy
    • 1
  • S. Miralles
    • 1
  • P. Moreno
    • 2
  • L. Navarro
    • 2
  • V. Pallas
    • 1
  • M. A. Perez-Amador
    • 1
  • J. Perez-Valle
    • 1
  • C. Pons
    • 1
  • I. Rodrigo
    • 1
  • P. L. Rodriguez
    • 1
  • C. Royo
    • 1
  • R. Serrano
    • 1
  • G. Soler
    • 2
  • F. Tadeo
    • 2
  • M. Talon
    • 2
  • J. Terol
    • 2
  • M. Trenor
    • 1
  • L. Vaello
    • 1
  • O. Vicente
    • 1
  • Ch. Vidal
    • 1
  • L. Zacarias
    • 3
  • V. Conejero
    • 1
    Email author
  1. 1.Instituto de Biologíia Molecular y Celular de Plantas (IBMCP)Universidad Politécnica de Valencia, Laboratorio de GenómicaValenciaSpain
  2. 2.Instituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
  3. 3.Instituto de Agroquímica y Tecnología de Alimentos (IATA)BurjasotSpain

Personalised recommendations