A New Reference Genome Shows the One-Speed Genome Structure of the Barley PathogenRamularia collo-cygni

Abstract

Ramularia leaf spot has recently emerged as a major threat to barley production world-wide, causing 25% yield loss in many barley growing regions. Here, we provide a new reference genome of the causal agent, the Dothideomycete Ramularia collo-cygni. The assembly of 32 Mb consists of 78 scaffolds. We used RNA-seq to identify 11,622 genes of which 1,303 and 282 are coding for predicted secreted proteins and putative effectors respectively.The pathogen separated from its nearest sequenced relative, Zymoseptoria tritici ∼27 Ma. We calculated the divergence of the two species on protein level and see remarkably high synonymous and nonsynonymous divergence. Unlike in many other plant pathogens, the comparisons of transposable elements and gene distributions, show a very homogeneous genome for R. collo-cygni. We see no evidence for higher selective pressure on putative effectors or other secreted proteins and repetitive sequences are spread evenly across the scaffolds. These findings could be associated to the predominantly endophytic life-style of the pathogen. We hypothesize that R. collo-cygni only recently became pathogenic and that therefore its genome does not yet show the typical pathogen characteristics. Because of its high scaffold length and improved CDS annotations, our new reference sequence provides a valuable resource for the community for future comparative genomics and population genetics studies.

Chromosomal rearrangements with stable repertoires of genes and transposable elements in an invasive forest-pathogenic fungus

“…The concept of “two-speed genome”, assuming that genes involved in host-pathogen interaction like CSEPS, would be clustered together in regions having a rapid evolution due to the presence of active TEs in their neighborhood, is indeed widely debated in fungi (Frantzeskakis, 2019; Torres et al, 2020). Our analysis, more consistent with a low gene compartmentalization and no significant change in CSEP and SM repertoires, is like what has been described in another plant fungal pathogen of natural ecosystems (Hartmann et al 2018), but also for other fungal species infecting crops (Stam et al, 2018; Schwessinger et al, 2018).…”

“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?

“…Correspondingly, the species studied by these techniques have rapidly spread from a few species with historically high economic and scientific relevance to species with local or recent impact. A good example is ash-dieback and Ramularia leaf spot (Saunders et al, 2014;Stam et al, 2018). There are clear differences in the strategies adopted to combat haustorial biotrophic and narrow-host range necrotrophic plant pathogens (Oliver, 2009;Burdon et al, 2014).…”

Fungicide strategies and resistance of Ramularia collo-cygni to demethylation and succinate dehydrogenase inhibitors in Austrian winter barley (Hordeum vulgare)

“…Several DMI studies in wheat showed that the application of different DMI fungicides were responsible for an increase in frequency of CYP51 mutations (Heick et al 2017;Stammler et al 2008). Gutiérrez-Alonso et al (2017) reported that high SDHI dose rates can reduce Septoria leaf blotch (caused by Z. tritici, with R. collo-cygni being the nearest sequenced relative according to Stam et al 2018). However, lower dose rates may reduce selection for resistance strains.…”