Identifying beneficial plant-microbial interactions using multi-omic approaches

In this project we will test the hypothesis that endophytes have reduced genomes optimised for symbiosis and with benefits to the plant, including increasing yield and/or resilience to abiotic stresses. Objectives: 1. Whole genome comparisons of novel cultured endophytes with free-living/pathogenic relatives. 2. Metabolomic analysis of endophytes in culture and in planta using laser assisted rapid evaporative ionisation mass spectrometry (REIMS). 3. Integrating genomic and metabolomic data sets to identify specific pathways over- and underrepresented in endophytes. 4. Association of metabolic pathways with plant growth promotion in planta with and without abiotic stress. Initially, the project will refine the genome assemblies, including strategically performing additional sequencing to generate longer assembled sequences where required. Once the genome assemblies have been refined, an optimal subset will be selected to study the genome modification/reduction. The endophyte genomes will be compared to their wild and pathogenic relatives, using sequences already in public repositories such as the NCBI. Differences in chromosome structure, operon structure, mobile elements, and genes under evolutionary selection pressure (identified by the ratio of synonymous to nonsynonymous sequence mutations) will be investigated to gain insight into the different evolutionary forces acting on these endophytes. Metabolomics experiments will provide additional evidence about the key genes, enzymes and metabolic pathways impacted by this process. Moreover, by identifying important metabolic pathways that are missing in the endophyte genomes it will be possible to infer which metabolites the endophytes acquire from their host; and the metabolic cross-talk within the endophyte populations can be elucidated. Finally, informatics predictions will be validated and refined with in planta experiments.