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

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.

Physiology of citrus fruiting

“…Thus, the combination of these characteristics suggests that the study of citrus fruit growth may reveal original regulation mechanisms based on specific molecular differences and/ or even novel genes (Forment et al, 2005;Cercós et al, 2006;Terol et al, 2007).…”

In silico prediction of gene expression patterns in Citrus flavedo

“…Particular interest has been paid to fruit genes and gene products involved in the flavonoids, vitamins, and organic acid biosynthesis, among others (Moriguchi et al, 1999;Matella et al, 2005;Shimada et al, 2006). However, to our knowledge, the only genomewide study involving citrus ESTs that contains flavedo sequences already published included 5,604 ESTs from Citrus clementina fruits (Forment et al, 2005). This number, although significant, is approximately 10-fold lower than the 51,729 valid C. sinensis flavedo EST sequences from the CitEST Project, a Brazilian initiative coordinated by the Centro APTA Citros Sylvio Moreira.…”

Closely-related Xanthomonas citri subsp. citri isolates trigger distinct histological and transcriptional responses in Citrus limon

“…Recently, new findings have provided insights into the roles of alternative splicing in the regulation of expression of plant defense genes (Marone et al, 2013). This factor has been generally associated with abiotic stresses such as cold and salinity (Forment et al, 2005;Iida et al, 2004); however, this is the first report of this gene in association with a biotic factor.…”