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

TitleDevelopment of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies
Publication TypeJournal Article
Year of Publication2005
AuthorsForment, J, Gadea, J, Huerta, L, Abizanda, L, Agusti, J, Alamar, S, Alos, E, Andres, F, Arribas, R, Beltran, JP, Berbel, A, Blazquez, MA, Brumos, J, Canas, LA, Cercos, M, Colmenero-Flores, JM, Conesa, A, Estables, B, Gandia, M, Garcia-Martinez, JL, Gimeno, J, Gisbert, A, Gomez, G, Gonzalez-Candelas, L, Granell, A, Guerri, J, Lafuente, MT, Madueno, F, Marcos, JF, Marques, MC, Martinez, F, Martinez-Godoy, MA, Miralles, S, Moreno, P, Navarro, L, Pallas, V, Perez-Amador, MA, Perez-Valle, J, Pons, C, Rodrigo, I, Rodriguez, PL, Royo, C, Serrano, R, Soler, G, Tadeo, F, Talon, M, Terol, J, Trenor, M, Vaello, L, Vicente, O, Vidal, C, Zacarias, L, Conejero, V
JournalPlant Mol Biol
KeywordsCitrus/*genetics DNA; Complementary/chemistry/genetics *Expressed Sequence Tags Gene Expression Profiling Gene Library *Genome; DNA; Plant Genomics/*methods Molecular Sequence Data Oligonucleotide Array Sequence Analysis/*methods RNA; Plant/genetics/metabolism Reproducibility of Results Sequence Analysis

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.


Forment, J Gadea, J Huerta, L Abizanda, L Agusti, J Alamar, S Alos, E Andres, F Arribas, R Beltran, J P Berbel, A Blazquez, M A Brumos, J Canas, L A Cercos, M Colmenero-Flores, J M Conesa, A Estables, B Gandia, M Garcia-Martinez, J L Gimeno, J Gisbert, A Gomez, G Gonzalez-Candelas, L Granell, A Guerri, J Lafuente, M T Madueno, F Marcos, J F Marques, M C Martinez, F Martinez-Godoy, M A Miralles, S Moreno, P Navarro, L Pallas, V Perez-Amador, M A Perez-Valle, J Pons, C Rodrigo, I Rodriguez, P L Royo, C Serrano, R Soler, G Tadeo, F Talon, M Terol, J Trenor, M Vaello, L Vicente, O Vidal, Ch Zacarias, L Conejero, V Comparative Study Research Support, U.S. Gov’t, Non-P.H.S. Netherlands Plant molecular biology Plant Mol Biol. 2005 Feb;57(3):375-91.