The Colletotrichum orchidophilum genome sequence: an example of how closely related species improve pan-genome analyses in fungal plant pathogens

Many species belonging to the genus Colletotrichum are associated with plant diseases, commonly referred to as anthracnose. Colletotrichum spp. can affect a wide range of hosts and these pathogens are characterized by a global distribution. In addition to its economic impact, Colletotrichum is one of the most studied genera of plant pathogenic fungi. Colletotrichum orchidophilum is a plant pathogenic fungus infecting a wide range of plant species belonging to the family Orchidaceae. C. orchidophilum has been used in recent years in evolutionary studies to study evolution and host specialization in plant pathogens, as it represents the closest related species to the C. acutatum (CA) species complex. Here we present the first draft whole-genome sequence of C. orchidophilum IMI 309357, providing a platform for future research on anthracnose of Orchidaceae and for evolutionary analyses of other Colletotrichum spp. The C. orchidophilum genome assembly consists of 321 scaffolds and encodes 14,496 proteins. We compared the newly sequenced genome with all Colletotrichum genomes publically available investigating the need for higher resolution taxonomic sampling for comparative genomics. Our results show that C. orchidophilum shares 85,4 % of the proteins with other CA species and the number of shared proteins is strongly correlated with phylogenetic distance. Further analyses revealed that 1564 have a predicted secretion signal peptide and of those 86 are Colletotrichum specific and 76 are unique to C. orchidophilum. Phylogenetic analyses of specific gene families (such the GH43) show that gene loss in C. orchidophilum is an important force driving the evolution of gene family size. This study also shows that major phenotypic changes are associated with comparatively recent changes in gene content.