title: Transcriptome response of Lolium arundinaceum to its fungal endophyte Epichloë coenophiala.
abstract: Tall fescue (Lolium arundinaceum) is one of the primary forage and turf grasses in temperate regions of the world. A number of favourable characteristics of tall fescue are enhanced by its seed-transmissible fungal symbiont (endophyte) Epichloë coenophiala. Our approach was to assemble the tall fescue transcriptome, then identify differentially expressed genes (DEGs) for endophyte-symbiotic (E+) vs endophyte-free (E-) clones in leaf blades, pseudostems, crowns and roots. RNA-seq reads were used to construct a tall fescue reference transcriptome and compare gene expression profiles. Over all tissues examined, 478 DEGs were identified between the E+ and E- clones for at least one tissue (more than two-fold; P < 0.0001, 238 E+ > E- and 240 E- > E+), although no genes were differentially expressed in all four tissues. Gene ontology (GO) terms, GO:0010200 (response to chitin), GO:0002679 (respiratory burst during defence response) and GO:0035556 (intracellular signal transduction) were significantly overrepresented among 25 E- > E+ DEGs in leaf blade, and a number of other DEGs were associated with defence and abiotic response. In particular, endophyte effects on various WRKY transcription factors may have implications for symbiotic stability, endophyte distribution in the plant, or defence against pathogens.
authors.affiliation: Forage-Animal Production Research Unit, USDA-ARS, Lexington, KY, 40546-0091, USA.
authors.forename: Randy D
authors.initials: RD
authors.lastname: Dinkins
authors.affiliation: Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546-0312, USA.
authors.forename: Padmaja
authors.initials: P
authors.lastname: Nagabhyru
authors.affiliation: Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Graham
authors.affiliation: Jamie Whitten Delta States Research Center, USDA-ARS, Stoneville, MS, 38776, USA.
authors.forename: Deborah
authors.initials: D
authors.lastname: Boykin
authors.affiliation: Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546-0312, USA.
authors.forename: Christopher L
authors.identifier: 0000-0003-2197-0842
authors.initials: CL
authors.lastname: Schardl
mesh_terms: D060026:Endophytes / Q000502:physiology*; D055329:Epichloe / Q000502:physiology*; D018506:Gene Expression Regulation, Plant; D008129:Lolium / Q000235:genetics* / Q000382:microbiology*; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012333:RNA, Messenger
keywords: 
  Epichloë coenophiala
  ; 
  Lolium arundinaceum
  ; RNA-seq; differential expression; transcriptome