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Open Access item MELOGEN: an EST database for melon functional genomics
Blanca, José M.
Aranda, Miguel A.
|Citation:||BMC Genomics. 2007; 8: 306|
|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.
|Description:||This article is available from: http://www.biomedcentral.com/1471-2164/8/306|
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