Pangenome, phylogenomics, and comparative genomics of Claviceps purpurea and the Claviceps genus

The genus Claviceps includes many strict ovarian parasites of Poaceae globally. Some species, such as C. purpurea are defensive mutualists or weak pathogens which can infect 400+ species while others, like C. africana are aggressive pathogens and have a very restrictive host range. Recent taxonomic advances in this genus have delimited cryptic species and separate lineages. The genus Claviceps represents an excellent system to study the evolution of fungal species that share identical infection patterns, but vary in aggressiveness and host range. The goal of this project was to sequence and assemble and annotate the genomes of 21 Claviceps species and 24 isolates of C. purpurea (for a total of 50 new genome assemblies) to better understand the recent divergence in host adaptation and to identify genes under selective pressure to understand the main evolutionary forces shaping the genus. Re-assembly was performed on nine previously published raw reads to standardize the results for this comparative genomic analysis.