title: Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome.
abstract: BACKGROUND
  Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Biosciences Division, Argonne National Laboratory, Lemont, IL 60490, USA. plarsen@anl.gov
authors.forename: Peter E
authors.initials: PE
authors.lastname: Larsen
authors.forename: Avinash
authors.initials: A
authors.lastname: Sreedasyam
authors.forename: Geetika
authors.initials: G
authors.lastname: Trivedi
authors.forename: Gopi K
authors.initials: GK
authors.lastname: Podila
authors.forename: Leland J
authors.initials: LJ
authors.lastname: Cseke
authors.forename: Frank R
authors.initials: FR
authors.lastname: Collart
mesh_terms: D002244:Carbon / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D017753:Ecosystem; D005632:Fructose / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D005947:Glucose / Q000737:chemistry; D055442:Metabolome; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D038821:Mycorrhizae / Q000235:genetics* / Q000502:physiology*; D010788:Photosynthesis; D018517:Plant Roots / Q000382:microbiology; D015398:Signal Transduction; D012988:Soil Microbiology; D049490:Systems Biology
chemical_list: D005632:Fructose; D002244:Carbon; D005947:Glucose