Transcriptome Analysis of Tall Fescue Endophyte-Infected Tissues Under Stress Conditions

Tall fescue (Lolium arundinaceum) plants symbiotic with the endophytic fungus, Epichloe coenophiala , (E+), have been shown to have better survivability and persistence than plants lacking the endophyte (E-).  To understand more about the grass-endophyte interactions and how endophyte affects the host plant physiology and gene expression, we have analyzed gene expression in different tissues (leaf, pseudostem, crown and roots) of a genetically identical E+ and E- clone grown in the greenhouse using RNA-Seq technology.  An in house tall fescue transcriptome assembly was generated using the RNA-Seq reads from different tissue/endophyte combinations using Trinity at iPlantCollaborative.org, and mapping onto the assembly was done using CLC Genomics Workbench.  Analysis of differential gene expression was done using JMP Genomics and significant differences were calculated using a False Discovery Rate at α< 0.05 where significant differences (>2-fold; P<0.0001) were calculated using computed adjustments for each comparison separately.  Over all the tissues examined, 478 unigenes were differentially expressed between the E+ and E- tissues (>2-fold; P<0.0001), 179 E+>E- and 222 E->E+.  No unigene was differentially expressed across the four tissues.  Gene ontology terms, GO:0010200 (response to chitin), GO:0002679 (respiratory burst during defense response) and GO:0035556 (intracellular signal transduction) were significantly over-represented involving 25 E->E+ DEG’s in the leaf tissue, although a number of the other unigenes determined as DEG’s were also associated with defense and abiotic response.