Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

Abstract

BackgroundPowdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare).ResultsThe near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome.ConclusionsThe characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.

High Humidity Causes Abnormalities in the Process of Appressorial Formation of Blumeria graminis f. sp. hordei

“…Our findings will contribute not only to the understanding of infection behaviors of Bgh in field conditions that are significantly affected by rainy weather but also to the elucidation of the functions of proteins secreted from the appressorium. In fact, the identification of cell wall degrading enzymes, which are thought to be contained in the secretions from the tip of appressorium, has been attempted to be identified previously [4,13]; however, these genes have not yet been found even though the whole genome of Bgh had been sequenced [14,15]. Moreover, there is no report on effector proteins secreted from the appressorium, although several candidates for secreted effector proteins (CSEPs) have been reported as effector proteins by omics analyses of the isolated haustoria [16][17][18].…”

Cross-Kingdom RNAi of Pathogen Effectors Leads to Quantitative Adult Plant Resistance in Wheat

“…tritici and B.g. hordei, and in the respective host genomes, wheat and barley (Mascher et al, 2017;Frantzeskakis et al, 2018;International Wheat Genome Sequencing Consortium, 2018;Müller et al, 2019). Additionally, CDS files of manually annotated SvrPm3 a1/f 1 family members were used for target prediction in the isolate Bgt_JIW2.…”

“…The B. graminis genomes encode one of the largest repertoires of effectors in fungi, consisting of over 800 annotated proteins (Bourras et al, 2018;Frantzeskakis et al, 2018;Müller et al, 2019). Transient HIGS has been successfully used to functionally validate such candidate virulence factors in barley powdery mildew (B. graminis f. sp.…”

Peer Review #1 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"

“…For example, some CNVs evolve so quickly that they can be used with success at the subindividual level, for example, in tracking clonal evolution of cancer cells using CNV-specific phylogenetic methods (e.g., Schwartz & Schäffer, 2017;Liang, Liao & Zhu, 2017;Ricketts et al, 2018;Urrutia et al, 2018). Moreover, their interspecific variation has been shown to correlate with the phylogeny of some groups, such as the highly pathogenic and rapidly-evolving barley powdery mildews (Frantzeskakis et al, 2018). However, such fast evolution may mean that these markers might be less useful at higher levels of biological organization.…”