Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs

Abstract

Host specialization by pathogens requires a repertoire of virulence factors as well as fine-tuned regulation of gene expression. The fungal wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a powerful model system for the discovery of genetic elements that underlie virulence and host specialization. We transcriptionally profiled the early stages of Z. tritici infection of a compatible host (wheat) and a noncompatible host (Brachypodium distachyon). The results revealed infection regulatory programs common to both hosts and genes with striking wheat-specific expression, with many of the latter showing sequence signatures of positive selection along the Z. tritici lineage. Genes specifically regulated during infection of wheat populated two large clusters of coregulated genes that may represent candidate pathogenicity islands. On evolutionarily labile, repeat-rich accessory chromosomes (ACs), we identified hundreds of highly expressed genes with signatures of evolutionary constraint and putative biological function. Phylogenetic analyses suggested that gene duplication events on these ACs were rare and largely preceded the diversification of Zymoseptoria species. Together, our data highlight the likely relevance for fungal growth and virulence of hundreds of Z. tritici genes, deepening the annotation and functional inference of the genes of this model pathogen.

Transcriptome and Metabolite Profiling of the Infection Cycle ofZymoseptoria triticion Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition

“…3B). This observation was true for all samples at every time point (Supplemental Table S3), thus confirming that the low expression previously reported for growth in one axenic culture and one time point of infection (Kellner et al, 2014) is in fact seen throughout the entire asexual infection cycle (as sampled here) and in at least two additional culture media. Overall, this suggests that the expression of genes residing on the accessory chromosomes is significantly weaker at all phases of the pathogen's asexual life cycle in host tissue.…”

“…3A, inset). This region currently contains 139 predicted genes and also was seen to have low overall expression at 4 dpi in an independent study (Kellner et al, 2014). The lack of expression support from this region across all replicated plant infections suggests that high-level expression of these genes is not essential for any phase of colonization or asexual reproduction by Z. tritici.…”

“…Three previous reports have used nextgeneration RNAseq to study aspects of this interaction (Brunner et al, 2013;Yang et al, 2013;Kellner et al, 2014). Brunner et al (2013) studied the expression of putative plant cell wall-attacking enzymes at three phases of infection by the isolate ST99CH3D7 of Z. tritici (not the publicly available reference isolate IPO323) and demonstrated that the majority were strongly expressed during the necrotrophic phase.…”

“…in culture), precluding the identification of fungal genes and processes up-regulated specifically during infection, (4) the absence of samples representing very early phases of the interaction, and (5) the lack of analysis of the later phases of advanced necrotrophic colonization and asexual pathogen reproduction. Finally, Kellner et al (2014) described an analysis of the Z. tritici transcriptome in axenic culture and also at a single time point of plant infection (during symptomless growth at 4 dpi) of wheat and a nonhost plant. A notable observation from this work was that, in general, genes residing on the eight smallest accessory chromosomes were expressed at a relatively low level (although differential expression was reported for some) compared with those on the larger core chromosomes 1 to 13.…”

Is Zymoseptoria tritici a hemibiotroph?

“…Interestingly, fungal mutualists, including the ectomycorrhizal fungi Laccaria bicolor and Tuber melanosporum, and biotrophic pathogens such as B. graminis also have a reduced number of PCWDEs (Tisserant et al, 2013;Martin et al, 2008Martin et al, , 2010Spanu et al, 2010;Balestrini and Bonfante, 2014). Once the nutrients are released, their uptake may be achieved by sugar and amino acid transporters such as major facilitator transporters that are specifically expressed in the asymptomatic phase (Keon et al, 2007;Yang et al, 2013;Brunner et al, 2013;Kellner et al, 2014;Torriani et al, personal communication). This is a common strategy used by biotrophic and hemibiotrophic pathogens, such as Ustilago spp.…”