title: Comparative transcriptomic analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles.
abstract: Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. The disease interaction is characterized by clearly defined temporal phases of infection, ultimately resulting in the death of host tissue. Zymoseptoria tritici is a highly polymorphic species with significant intraspecific variation in virulence profiles. We generated a deep transcriptomic sequencing dataset spanning the entire time course of an infection using a previously uncharacterized, highly virulent Z. tritici strain isolated from a Swiss wheat field. We found that seven clusters of gene transcription profiles explained the progression of the infection. The earliest highly up-regulated genes included chloroperoxidases, which may help the fungus cope with plant defences. The onset of necrotrophy was characterized by a concerted up-regulation of proteases, plant cell wall-degrading enzymes and lipases. Functions related to nutrition and growth characterized late necrotrophy and the transition to saprotrophic growth on dead plant tissue. We found that the peak up-regulation of genes essential for mating coincided with the necrotrophic phase. We performed an intraspecies comparative transcriptomics analysis using a comparable time course infection experiment of the genome reference isolate IPO323. Major components of the fungal infection transcriptome were conserved between the two strains. However, individual small, secreted proteins, proteases and cell wall-degrading enzymes showed strongly differentiated transcriptional profiles between isolates. Our analyses illustrate that successful STB infections involve complex transcriptomic remodelling to up-regulate distinct gene functions. Heterogeneity in transcriptomes among isolates may explain some of the considerable variation in virulence and host specialization found within the species.
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.
authors.forename: Javier
authors.initials: J
authors.lastname: Palma-Guerrero
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.|Syngenta Crop Protection AG, Schaffhauserstrasse, 4332, Stein, Switzerland.
authors.forename: Stefano F F
authors.initials: SF
authors.lastname: Torriani
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.
authors.forename: Marcello
authors.initials: M
authors.lastname: Zala
authors.affiliation: School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia.
authors.forename: Dee
authors.initials: D
authors.lastname: Carter
authors.affiliation: Syngenta Crop Protection AG, Schaffhauserstrasse, 4332, Stein, Switzerland.
authors.forename: Mikaël
authors.initials: M
authors.lastname: Courbot
authors.affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
authors.forename: Jason J
authors.initials: JJ
authors.lastname: Rudd
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: McDonald
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Croll
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000472:pathogenicity; D002473:Cell Wall / Q000378:metabolism; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D063990:Gene Ontology; D005800:Genes, Fungal; D010935:Plant Diseases / Q000382:microbiology; D018515:Plant Leaves / Q000382:microbiology; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D013997:Time Factors; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*; D014908:Triticum / Q000382:microbiology; D015854:Up-Regulation / Q000235:genetics; D014774:Virulence / Q000235:genetics
keywords: RNA sequencing; Septoria leaf blotch; Zymoseptoria tritici; comparative transcriptomics; hemibiotroph