Transcriptome response of Lolium arundinaceum to the fungal endophyte Epichloe coenophiala

Authors: Dinkins, Randy; NAGABHYRU, P - University Of Kentucky; Graham, Michelle; Boykin, Deborah; SCHARDL, C - University Of Kentucky

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2016
Publication Date: 8/1/2016
Citation: Dinkins, R.D., Nagabhyru, P., Graham, M.A., Boykin, D.L., Schardl, C.L. 2016. Transcriptome response of Lolium arundinaceum to the fungal endophyte Epichloe coenophiala. New Phytologist. doi: 10.1111/nph.14103.

Interpretive Summary: Tall fescue (Lolium arundinaceum) is one of the principal cool-season species used as a forage and turf within the USA. A number of benefits associated with the persistence of tall fescue have been attributed to the presence of its seed-transmissible symbiont, the fungal endophyte Epichloë coenophiala. To date no metabolite, or compound, has been found to be involved in the crosstalk between the fungal endophyte and plant. Our approach was to utilize Next Generation Sequencing (NGS) technology to determine whether specific differentially expressed genes (DEG’s) might provide clues as to the putative crosstalk signal. NGS sequencing was used to construct a tall fescue reference gene assembly. The Illumina RNA-Seq reads were then used to compare gene expression in endophyte-infected (E+) and endophyte-free (E-) tissues of a genetically identical tall fescue clone to identify differentially expressed transcripts. Eighty putative genes were differentially expressed specifically between the E+ and E- tissues, 67 in the leaves, 5 in the pseudostem, 2 in the crown tissues and 12 in the roots. No gene was differentially expressed across the four tissues, although six were found across two tissues, four across leaf and root, one across leaf and pseudostem and one across the pseudostem and crown tissues. Of the 80 DEG’s only three were more highly expressed in the endophyte-infected (E+) tissues. A number of the genes differentially expressed are associated with pathogen defense and stress responses. Our results suggest that the presence of the endophyte is functioning in a protective role against potential pathogens as the observed the putative differentially expressed genes, are either directly repressed by E. coenophiala in the E+ plants that would have the consequence of inhibiting pathogen colonization, or the presence of other fungal or bacterial species induced these genes in the E- plants. Since disease conditions was not monitored in the plants utilized in the experiment, additional work will be needed to distinguish between the two possibilities.

Technical Abstract: Tall fescue (Lolium arundinaceum) is one of the principal cool-season species used as a forage and turf within the USA. A number of benefits associated with the persistence of tall fescue have been attributed to the presence of its seed-transmissible symbiont, the fungal endophyte Epichloë coenophiala. To date no metabolite, or compound, has been found to be involved in the host-endophyte crosstalk. Our approach was to interrogate the tall fescue transcriptome to determine whether specific differentially expressed genes (DEG’s) might provide clues as to the putative crosstalk signal. RNA-Seq reads were used to construct a tall fescue reference transcriptome and compare gene expression in endophyte-harboring (E+) and endophyte-free (E-) tissues of a genetically identical tall fescue clone to identify differentially expressed transcripts. Eighty unigenes were differentially expressed specifically between the E+ and E- tissues (>2-fold; P<0.0001), 67 in the leaves, 5 in the pseudostem, 2 in the crown tissues and 12 in the roots. No unigene was differentially expressed across the four tissues, although six were found across two tissues, four across leaf and root, one across leaf and pseudostem and one across the pseudostem and crown tissues. Of the 80 DEG’s only three were more highly expressed in the E+ tissues. One gene ontology term was found to be significant involving six DEG’s, GO:0002679 (respiratory burst during defense response), in the leaf tissue, although a number of the other unigenes determined as DEG’s were also associated with defense and abiotic response. It is well established that E. coenophiala produced alkaloids are toxic to mammals and insects. Our results suggest that the presence of the endophyte is also functioning in a protective role against potential pathogens as the observed DEG’s are either directly repressed by E. coenophiala in the E+ plants that would have the consequence of inhibiting colonization, or the presence of other species induced these genes in the E- plants.