Fungal symbionts generate water-saver and water-spender plant drought strategies via diverse effects on host gene expression

Panicum hallii var hallii HAL2 plants were inoculated individually with six foliar fungal endophytes or fungus-free controls and subjected to 5% or 20% soil moisture treatments. The fungi were selected for their previously observed effects on plant drought physiology, inducing either a “water saver” or a “water spender” strategy in the host. Plants were grown in enclosed microcosms to prevent cross-contamination and each treatment and control included 6 replicates. All fungi were Ascomycetes isolated from plants in central Texas. Plants were monitored for height, wilt, water loss, and survival. At the harvest, we also measured biomass and leaf colonization by the fungi and flash-froze leaf tissue for transcriptomic analyses. Both plant response and gene expression data are provided., Plants were grown in microcosms with fungal inocula or fungus-free controls, under drought (5% gravimetric) or well-watered (20% gravimetric) soil moisture. Every 3 days, plants were measured for height, wilt resistance (days to first wilt), and survival (days to first tiller death). Microcosms were also weighed for whole-plant water loss, and water was added as needed to maintain treatments. Relative height growth rate (RGR) and water loss rate were calculated from the repeated measurements as the change over time. After application of the water treatments for 21 days, three replicates were used to measure fungal leaf colonization rates. The remaining three replicates from each treatment were harvested for RNAseq by flash-freezing in liquid N2 immediately after measuring fresh weight. 
Read number and quality of the RNA-seq libraries were determined with FastQC. To analyze the RNA-seq libraries, reads of each sample were mapped to the Panicum hallii var hallii HAL2 genotype v2.1 refere...,