The evolutionary history of global Ramularia collo-cygni epidemics

Remco Stam 1 Hind Sghyer 1 Martin Münsterkötter 2 Aurelien Tellier 4 Ralph Hückelhoven 1 Ulrich Güldener 3 Michael Heß 1
1Chair of Phytopathology, Technical University of Munich, Freising, Germany
2Institute of Bioinformatics and Systems Biology, Helmholtz Centre Munich, GroƟhadern, Germany
3Department of Genome-oriented Bioinformatics, Technical University of Munich, Freising, Germany
4Section of Population Genetics, Technical University of Munich, Freising, Germany

Ramularia Leaf Spot (RLS) has emerged as a global threat for barley production. Late appearance of unspecific RLS symptoms made that only with molecular diagnostics the fungus Ramularia collo-cygni (Rcc) could be detected as the biotic factor of disease. Recent research has shed more light on the biology and genomics of the pathogen, the cause of the recent global spread remains unclear.

To address urging questions, about life-cycle, transmission, and quick adaptation to control measures, we de-novo sequenced the genome of Rcc. Additionally, we sequenced fungal RNA from 6 different conditions to improve annotation. This resulted in a high quality draft assembly of about 32 Mb, with only 78 scaffolds (N50: 2.1 Mb). The overall annotation enabled the prediction of 12.346 high confidence genes. Genomic comparison revealed that Rcc has significantly diverged from related Dothidiomycetes, however without obtaining species-specific genome features.

To evaluate the species-wide genetic diversity, we resequenced the genomes of 19 Rcc isolates from multiple geographic locations and diverse hosts and mapped sequences to our reference genome. Admixture analyses show that Rcc is world-wide genetically uniform and that samples do not show a strong clustering on either geographical location or host species. Most samples cluster closely together, with the exception of three outliers.

Analysis of linkage disequilibrium shows that in the world-wide sample set there are signals of recombination and thus sexual reproduction, however these signals largely disappear when excluding the three outliers samples, suggesting that the main global expansion of Rcc comes from clonally propagating populations. We further analysed the historic population size (Ne) of Rcc using Bayesian simulations, which provides additional indicators for the timing of population expansions.

Ultimately, we discuss how recombination, clonal spreading and lack of host-specificity could further support global epidemics and place Rcc the category of high-risk plant pathogen.