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Open Access Highly Accessed Research article

MELOGEN: an EST database for melon functional genomics

Daniel Gonzalez-Ibeas1, José Blanca2, Cristina Roig2, Mireia González-To3, Belén Picó2, Verónica Truniger1, Pedro Gómez1, Wim Deleu3, Ana Caño-Delgado4, Pere Arús3, Fernando Nuez2, Jordi Garcia-Mas3, Pere Puigdomènech4 and Miguel A Aranda1*

Author Affiliations

1 Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain

2 Departamento de Biotecnología, Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain

3 Departament de Genètica Vegetal, Centre de Recerca en Agrigenòmica CSIC-IRTA, Carretera de Cabrils Km2, 08348 Cabrils (Barcelona), Spain

4 Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica CSIC-IRTA, Jordi Girona 18-26, 08034 Barcelona, Spain

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BMC Genomics 2007, 8:306  doi:10.1186/1471-2164-8-306

Published: 3 September 2007

Abstract

Background

Melon (Cucumis melo L.) is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential traits, such as fruit development, fruit maturation and disease resistance, and to speed up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs) from eight normalized cDNA libraries from different tissues in different physiological conditions.

Results

We determined over 30,000 ESTs that were clustered into 16,637 non-redundant sequences or unigenes, comprising 6,023 tentative consensus sequences (contigs) and 10,614 unclustered sequences (singletons). Many potential molecular markers were identified in the melon dataset: 1,052 potential simple sequence repeats (SSRs) and 356 single nucleotide polymorphisms (SNPs) were found. Sixty-nine percent of the melon unigenes showed a significant similarity with proteins in databases. Functional classification of the unigenes was carried out following the Gene Ontology scheme. In total, 9,402 unigenes were mapped to one or more ontology. Remarkably, the distributions of melon and Arabidopsis unigenes followed similar tendencies, suggesting that the melon dataset is representative of the whole melon transcriptome. Bioinformatic analyses primarily focused on potential precursors of melon micro RNAs (miRNAs) in the melon dataset, but many other genes potentially controlling disease resistance and fruit quality traits were also identified. Patterns of transcript accumulation were characterised by Real-Time-qPCR for 20 of these genes.

Conclusion

The collection of ESTs characterised here represents a substantial increase on the genetic information available for melon. A database (MELOGEN) which contains all EST sequences, contig images and several tools for analysis and data mining has been created. This set of sequences constitutes also the basis for an oligo-based microarray for melon that is being used in experiments to further analyse the melon transcriptome.