Transcriptome response ofLolium arundinaceumto its fungal endophyteEpichloë coenophiala

Abstract

SummaryTall 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) Epichlo€ e coenophiala.Our approach was to assemble the tall fescue transcriptome, then identify differentially expressed genes (DEGs) for endophyte-symbiotic (E+) vs endophyte-free (EÀ) 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 EÀ clones for at least one tissue (more than two-fold; P < 0.0001, 238 E+ > EÀ and 240 EÀ > 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 EÀ > 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.

Bacillus amyloliquefaciens alters gene expression, ROS production and lignin synthesis in cotton seedling roots

“…; Saha and Seal ; Dinkins et al . ). Studies on the genetic response triggered in plants by bacterial endophytes have mostly focused on gene expression of Arabidopsis thaliana inoculated with Pseudomonas fluorescens and Bacillus sp.…”

Transcriptome Analysis and Differential Expression in Tall Fescue Harboring Different Endophyte Strains in Response to Water Deficit

“…To remove the endophyte and tall fescue chloroplast reads, the filtered reads were mapped to the E. coenophiala e4163 and e19 strains genome assemblies (http://www.endophyte.uky.edu; Schardl et al, 2013b) and the tall fescue chloroplast sequence (GenBank: KM974751.1 [Saarela et al, 2015]) with minimum length fraction set to 0.9 and minimum similarity fraction set to 0.95. The unmapped reads were then mapped to tall fescue TF153K transcriptome assembly containing 153,321 unigenes (Dinkins et al, 2017) with minimum length fraction set to 0.9 and minimum similarity fraction set to 0.8. Reads were normalized by the Quantile method in CLC Genomics Workbench, and only unigenes that had at least one clone–endophyte–treatment combination with a minimum of 20 average mapped reads were used for differential expression analysis.…”

“…Biological processes and molecular function gene ontology (GO) terms were annotated to the TF153K tall fescue assembly based on the Arabidopsis gene annotations as described in Dinkins et al (2017). Gene lists associated with DEGs from the various treatments were compared with the TF153K unigene lists to identify overrepresented pathways using the custom input tool at the web‐based agriGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php) using the Fisher statistical test method, Bonferroni multitest adjustment method, and a cut‐off of 10 −5 (Tian et al, 2017).…”

“…& Samuels) C.W. Bacon & Schardl (Schmid et al, 2017), and tall fescue with E. coenophiala (Dinkins et al, 2010, 2017) and others (Ambrose and Belanger 2012) have indicated endophyte effects on host gene expression relevant to stress tolerance and responses to fungi.…”

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

“…In a comparative transcriptome analysis, a stress-responsive protein has been identified in Lolium/Festuca species (Czaban et al, 2015). Recently, transcriptome analyses were done to study dwarfism to enhance dwarfing breeding in Kentucky bluegrass (Gan et al, 2016), drought stress response in creeping bentgrass (Ma et al, 2017), water stress (Talukder et al, 2015), lead (pb) stress (Li et al, 2017), and endophyte response in tall fescue (Dinkins et al, 2017), and to develop a unigene reference as a molecular breeding resource in Phalaris (Baillie et al, 2017). Markers developed from the reference transcript corresponding to the protein might be useful for MAS for stress tolerance.…”