Combined 'omics approaches for the study of ectomycorrhizal symbiosis between Suillus and Pinaceae, with emphasis on their role in nutrient cycling
EMSL Project ID
49514
Abstract
This study will explore the genetics of obligately symbiotic interactions between conifers (Pinaceae) and their host-specific ectomycorrhizal fungi in the mushroom genus Suillus, and their effects on ecological cycling of forest carbon. Using conifer seedlings experimentally inoculated with different Suillus species, we will employ integrated metatranscriptomic / metaproteomic / metabolomic approaches identify key fungal in EMF-Pinaceae roots for the species represent samples of the widely co-distribution across their natural habitats. Here we request metatranscriptomic sequencing of root/rhizosphere soil samples using newly developed methods that preferentially enrich fungal and plant mRNA (JGI). Sequenced transcriptome reads will be mapped to Suillus genomes (curated by JGI) or plant reference EST databases (publicly available and/or sequenced during this project). Comparative meta'omics analysis (JGI/EMSL) will allow us to investigate the genetic basis of host specificity between compatible/incompatible species pairs of Suillus-Pinaceae, and also identify their roles in soil nutrient cycling. This study will provide the first ever assessment of molecular functioning and core genes involved in ectomycorrhizal formation at the genus and species level (Suillus) across a phylogenetically diverse sampling of conifers (Pinaceae). Meta'omic analyses of mycorrhizal functioning in soil will also help us to better define the roles these species play in soil nutrient turnover.
Scope of work: In collaboration with JGI & EMSL, the metatranscriptomes (JGI) metaproteomics (EMSL), metabolomics (EMSL), and image (EMSL) of whole EMF-plant root tips and their sectional tissues will be characterized across major species of Suillus and Pinaceae pairs. We will examine species of Suillus-Pinaceae pairs that are co- and widely distributed in the natural forest system. We request sequencing resources for ~300 Gb of 125PE Illumina RNAseq, including a) with JGI: 1 Gb for each sample unit of compatible pairs and 3 Gb for each sample unit of incompatible pairs, cDNA library construction, and data analysis through comparative metatranscriptomes; b) and with EMSL for proteomics/metabolomomics analysis and imaging of root tissues and rhizosphere soil for representative samples (48 samples).
Project Details
Project type
FICUS Research
Start Date
2016-10-01
End Date
2018-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members
Related Publications
Velickovic D., H. Liao, R. Vilgalys, R.K. Chu, and C.R. Anderton. 2019. "Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization." Journal of Natural Products 82, no. 5:1382-1386. PNNL-SA-140336. doi:10.1021/acs.jnatprod.8b01050