Abstract
BACKGROUND: Whole genome transcriptomics analysis is a very powerful
approach because it gives an overview of the activity of genes in
certain cells or tissue types. However, biological interpretation
of such results can be rather tedious. MapMan is a software tool
that displays large datasets (e.g. gene expression data) onto diagrams
of metabolic pathways or other processes and thus enables easier
interpretation of results. The grapevine (Vitis vinifera) genome
sequence has recently become available bringing a new dimension into
associated research. Two microarray platforms were designed based
on the TIGR Gene Index database and used in several physiological
studies. RESULTS: To enable easy and effective visualization of those
and further experiments, annotation of Vitis vinifera Gene Index
(VvGI version 5) to MapMan ontology was set up. Due to specificities
of grape physiology, we have created new pictorial representations
focusing on three selected pathways: carotenoid pathway, terpenoid
pathway and phenylpropanoid pathway, the products of these pathways
being important for wine aroma, flavour and colour, as well as plant
defence against pathogens. This new tool was validated on Affymetrix
microarrays data obtained during berry ripening and it allowed the
discovery of new aspects in process regulation. We here also present
results on transcriptional profiling of grape plantlets after exposal
to the fungal pathogen Eutypa lata using Operon microarrays including
visualization of results with MapMan. The data show that the genes
induced in infected plants, encode pathogenesis related proteins
and enzymes of the flavonoid metabolism, which are well known as
being responsive to fungal infection. CONCLUSION: The extension of
MapMan ontology to grapevine together with the newly constructed
pictorial representations for carotenoid, terpenoid and phenylpropanoid
metabolism provide an alternative approach to the analysis of grapevine
gene expression experiments performed with Affymetrix or Operon microarrays.
MapMan was first validated on an already published dataset and later
used to obtain an overview of transcriptional changes in a susceptible
grapevine - Eutypa lata interaction at the time of symptoms development,
where we showed that the responsive genes belong to families known
to be involved in the plant defence towards fungal infection (PR-proteins,
enzymes of the phenylpropanoid pathway).
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