Comparative genomics of cochliobolus phytopathogens

Cochliobolus is a young genus, in the class Dothideomycetes, which includes closely related plant pathogenic and saprophytic fungal species. In this review, genome similarities and differences among sequenced Cochliobolus pathogens that cause different diseases on different hosts are detailed. Gene content and genome organization are highly similar within the group and pathogens of the same host are not more similar to each other than those with different hosts. Instead, overarching genetic patterns follow phylogenetic lines. Classical and functional genetic research using Cochliobolus species has identified genes for secondary metabolism, management of iron and oxidative stress, and signaling as being involved in virulence. The genomic inventories and phylogenetic contexts of these genes, as well as of genes encoding protein effectors and cytochrome P450s, are compared across the genus, providing new insights into the evolution of host-specific virulence. Categorization of genes for secondary metabolism, according to distribution throughout the genus, is particularly revealing with unique genes tending to encode enzymes that biosynthesize metabolites involved in virulence. Additionally, genomic analysis identified many genes that encode unique small, secreted proteins, which could act as effectors in the plant host. Finally, new avenues for research paved by genomic analysis are highlighted.