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.

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.

Figure 1

Unigenes statistics. (A) Distribution of melon ESTs among unigenes (contigs and singletons). (B) Size distribution of melon unigenes.

Figure 2

Distribution of melon and Arabidopsis unigenes according to the Gene Ontology scheme for functional classification of gene products.

Figure 3

Potential precursors of melon microRNAs. (A) Stem loop sequence of putative precursor miRNA corresponding to unigene bCI_04-H02-M13R_c. (B) Stem loop sequence of putative precursor miRNA corresponding to unigene b15d_24-H05-M13R_c. The mature miRNA sequences are shown in bold.

Figure 4

Transcripts analyzed by Real Time qPCR. (A) Pattern of transcripts accumulation in CMV-infected melon cotyledons (CI) relative to that of healthy cotyledons (CS). (B) Pattern of transcripts accumulation in M. cannonballus infected roots of C. melo L. cv. "Piel de sapo" (PSI) relative to that of healthy roots (PS). (C) Pattern of transcripts accumulation in M. cannonballus infected roots of C. melo L. ssp. agrestis (AI) relative to that of healthy roots (A). (D) Pattern of transcripts accumulation in fruits of 15 days after pollination of C. melo L. cv. "Piel de sapo" (15d) relative to that of fruits of 46 days after pollination (46d). cy: cyclophilin endogenous control; see Table 9 for the rest of genes.