Exploring Symbiotic Genomes and Transcriptomes
PI : Annegret Kohler (UMR 1136 Interactions Arbre/Micro-organismes – IAM)
Co-applicants : Emmanuelle Morin (IAM), Francis Martin (IAM)
Collaboration : JOINT GENOME INSTITUTE (JGI), USA – Un Ingénieur d’étude (recruté dans le cadre de ce projet)
____________________________
Context — Mycorrhizal symbioses are mutualistic associations formed between plant roots and soil-borne fungi, which involve a multitude of plants and fungal species. In exchange for carbon, mycorrhizal fungi provide plants with different resources, including water, nitrogen or phosphorus. Yet the nature and regulation of the genes defining symbiosis still elude us. Mycorrhizal fungi connect plants to soil, plants to plants, microbes to plants, but still, we understand very little about the genetic code driving these connections.
Objectives — We propose to use already available genomes together with transcriptome sequencing (RNA-Seq) to explore symbiosis-related gene networks behind the development and functioning of ectomycorrhizal , ericoid and orchid symbioses. We will compare the transcriptomes of free-living fungi and of plant roots colonised by fungal strains, at the onset of colonisation and once the mycorrhizal structures have been established. We will focus our search to sequence data associated with plant-fungus signaling (effectors), primary metabolism, and degradation metabolism.
Approach — The bioinformatician hired by this project will be in charge of mining the transcriptomic data and to define a workflow for transcriptome analyses.
The main missions will be:
- gene expression quantification
- differential expression and coexpression networks analysis
- data visualization tools
Expected results and impacts — Data from ongoing genome sequencing projects at the Joint Genome Institute will be used in this project. The transcriptome analyses will add an additional value to the these data and will help to better understand the development and evolution of the mycorrhizal symbiosis.
