Exploring the transcriptome of roots and ectomycorrhizal symbionts

Annegret Kohler, Sébastien Duplessis, Denis Tagu, Nathalie Encelot, Christine Delaruelle and Francis Martin
UMR INRA-UHP 1136 Interactions Arbres/Micro-organismes, Centre INRA de Nancy, 54280 Champenoux

Ectomycorrhiza formation and function alter both fungal and plant gene expression. The identification of genes expressed in the symbiosis will contribute to the understanding of the function of the ectomycorrhizal association. Gene discovery by partial sequence determination of cDNA clones (ESTs) is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of root growth and development, including the impact of ectomycorrhizal symbiosis development. cDNA array experiments utilizing Eucalyptus globulus, Populus x interamericana, and the ectomycorrhizal basidiomycete Pisolithus tinctorius have been used to gain additional information about the potential roles of expressed genes in root and ectomycorrhiza formation.
Different statistical methods (i.e., hierarchical clustering, self organizing maps) have been used to analyse data from first-generation ectomycorrhiza and poplar root cDNA arrays: Predictions of differential gene expression between cDNA sequencing experiments (in silico Northern blots) and cDNA array experiments are in agreement and both approaches provide lists of candidate genes which should be further investigated for potential roles in root and symbiosis development.
As the number of ESTs increases, in silico comparisons across genera, species, ecotypes, and strains of symbiotic fungi will become possible. With multiple EST/cDNA array programmes dealing with pathogenic and mutualistic fungi, we will have in a near future an unparalleled opportunity to ask which genetic features are responsible for common/divergent traits involved in pathogenesis and symbiosis. A few of the many possible breakthroughts will be in characterisation of common transduction networks, identification of novel surface proteins that play critical roles in plant-fungus interactions and new insights into unique metabolic routes critical for mycorrhiza functioning.