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

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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.

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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

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Authors and Affiliations

  1. Instituto de Biologíia Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia, Laboratorio de Genómica, Avenida de los Naranjos, s/n, 46022, Valencia, Spain

    J. Forment, J. Gadea, L. Huerta, L. Abizanda, R. Arribas, J. P. Beltran, A. Berbel, M. A. Blazquez, L. A. Canas, J. L. Garcia-Martinez, J. Gimeno, A. Gisbert, G. Gomez, A. Granell, F. Madueno, M. C. Marques, M. A. Martinez-Godoy, S. Miralles, V. Pallas, M. A. Perez-Amador, J. Perez-Valle, C. Pons, I. Rodrigo, P. L. Rodriguez, C. Royo, R. Serrano, M. Trenor, L. Vaello, O. Vicente, Ch. Vidal & V. Conejero

  2. Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada-Náquera, Km.4.5, 46113, Moncada, Valencia, Spain

    J. Agusti, E. Alos, F. Andres, J. Brumos, M. Cercos, J. M. Colmenero-Flores, A. Conesa, M. Gandia, J. Guerri, F. Martinez, P. Moreno, L. Navarro, G. Soler, F. Tadeo, M. Talon & J. Terol

  3. Instituto de Agroquímica y Tecnología de Alimentos (IATA), Apdo. 73, 46100, Burjasot, Valencia, Spain

    S. Alamar, B. Estables, L. Gonzalez-Candelas, M. T. Lafuente, J. F. Marcos & L. Zacarias

Authors
  1. J. Forment
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  2. J. Gadea
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  3. L. Huerta
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  4. L. Abizanda
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  5. J. Agusti
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  6. S. Alamar
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  7. E. Alos
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  8. F. Andres
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  9. R. Arribas
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  10. J. P. Beltran
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  11. A. Berbel
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  12. M. A. Blazquez
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  13. J. Brumos
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  14. L. A. Canas
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  15. M. Cercos
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  16. J. M. Colmenero-Flores
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  17. A. Conesa
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  18. B. Estables
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  19. M. Gandia
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  20. J. L. Garcia-Martinez
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  21. J. Gimeno
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  22. A. Gisbert
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  23. G. Gomez
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  24. L. Gonzalez-Candelas
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  25. A. Granell
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  26. J. Guerri
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  27. M. T. Lafuente
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  28. F. Madueno
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  29. J. F. Marcos
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  30. M. C. Marques
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  31. F. Martinez
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  32. M. A. Martinez-Godoy
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  33. S. Miralles
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  34. P. Moreno
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  35. L. Navarro
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  36. V. Pallas
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  37. M. A. Perez-Amador
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  38. J. Perez-Valle
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  39. C. Pons
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  40. I. Rodrigo
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  41. P. L. Rodriguez
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  42. C. Royo
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  43. R. Serrano
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  44. G. Soler
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  45. F. Tadeo
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  46. M. Talon
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  47. J. Terol
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  48. M. Trenor
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  49. L. Vaello
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  50. O. Vicente
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  51. Ch. Vidal
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  52. L. Zacarias
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  53. V. Conejero
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Corresponding author

Correspondence to V. Conejero.

Additional information

†These authors contributed equally to this work.

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Forment, J., Gadea, J., Huerta, L. et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol 57, 375–391 (2005). https://doi.org/10.1007/s11103-004-7926-1

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