title: MELOGEN: an EST database for melon functional genomics.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: 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. agr030@cebas.csic.es
authors.forename: Daniel
authors.initials: D
authors.lastname: Gonzalez-Ibeas
authors.forename: José
authors.initials: J
authors.lastname: Blanca
authors.forename: Cristina
authors.initials: C
authors.lastname: Roig
authors.forename: Mireia
authors.initials: M
authors.lastname: González-To
authors.forename: Belén
authors.initials: B
authors.lastname: Picó
authors.forename: Verónica
authors.initials: V
authors.lastname: Truniger
authors.forename: Pedro
authors.initials: P
authors.lastname: Gómez
authors.forename: Wim
authors.initials: W
authors.lastname: Deleu
authors.forename: Ana
authors.initials: A
authors.lastname: Caño-Delgado
authors.forename: Pere
authors.initials: P
authors.lastname: Arús
authors.forename: Fernando
authors.initials: F
authors.lastname: Nuez
authors.forename: Jordi
authors.initials: J
authors.lastname: Garcia-Mas
authors.forename: Pere
authors.initials: P
authors.lastname: Puigdomènech
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Aranda
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D019662:Cucurbitaceae / Q000235:genetics*; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D018745:Genome, Plant; D023281:Genomics / Q000379:methods