Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose.The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.Within days of germination, 95% of the short roots of most conifers and deciduous trees form ectomycorrhizae (ECM) with soil fungi [1], a form of symbiosis between plants and fungi whose evolution dates back 360-410 million years [2]. In ectomycorrhizae, the fungus forms a mycelial sheath around the plant's root, called the Hartig net that isolates the root from the soil and inhibits the development of short root hairs. Nutrients are exchanged between fungus and root across the apoplast, a zone that is outside both root and fungus, preventing direct contact between the fungus and plant cytoplasm and requiring