Species phylogeny, amino acid similarity, and repeat content.

A) Maximum likelihood phylogenetic tree based on 51 conserved protein families showing evolutionary relationships of Cladosporium fulvum and Dothistroma septosporum. Branch lengths are indicated by the bar (substitutions/site); bootstrap values are shown as percentage. B) Genome-wide amino acid similarity of homologous proteins between C. fulvum and other sequenced fungal species. A pair of proteins is only reported as homologous when the predicted similarity (blastp) spans at least 70% of their lengths and their length difference is at most 20%. Axis indicates number of homologous proteins. Bar shading indicates similarity: red, 91–100%; orange, 81–90%; light green, 71–80%; medium green, 61–70%; turquoise, 51–60%; light blue, 41–50%; dark blue, 31–40%; and purple, 0–30%. Homologous proteins with high amino acid similarity are likely orthologs, whereas for those with lower similarity this relation cannot be inferred. C) Repeat content of C. fulvum, D. septosporum and other sequenced fungal species. Bar shading indicates repeat class: red, unique non-repeat regions; brown, repeat elements; green, continuous tracts of N characters; blue, duplicated regions; and grey, poorly assembled regions (C. fulvum only). Axis indicates number of nucleotides (Mb).