Given the rapidly increasing capacity for sequencing, as well as the decreasing cost, comparing the genomes of multiple strains and species has become an effective approach for uncovering genomic features that potentially underpin specific traits or ecological niches. In the March Focus Issue on genomics, Seidl et al. compare the gene repertoire and genome organization of Verticillium tricorpus with those of two pathogenic relatives: V. dahliae and V. alfalfae. These species encode similar putative effectors; thus, a key question is what functions these proteins confer.