Supplementary Figure S3 high resolution and comments from A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria

A Maximum Likelihood rooted tree of all available fungal XDH-like enzymes with Eukaryotic out-groups. Colour keys for fungal clades, metazoans and Ichthyosporea (Opisthokonta) are those given in figure 4. Archaeplastida and Stramenopiles, including green algae and plants (Viridiplantae), red algae (Rhodophyta), Oomycetes and Diatoms are at the bottom of the tree, indicated with different shades of green. In black with no additional colouring, representative species from other taxa: Thecamonas trahens (Apusozoa, Bikonta), Guillardia theta (Cryptophyta, Chromista), Dictyostelium discoideum (Amoebozoa, Unikonta), Trichomonas vaginalis (Parabasalia, Excavata), Trimastix pyriformis (Metamonada, Excavata). In red lettering we indicate proteins where biochemical work is extant (comprising 3D structural work for Bos taurus XDH). In green lettering we indicate proteins, which are in positions that do not correspond to the taxonomically appropriate position of the organism in question. Searches for genes encoding XDH-like proteins were carried out with both HxA and HxnS of A. nidulans as in silico probes. All fungal gene models and proteins were deduced manually. The auto-annotated accession numbers were curated as indicated in S1 Table (a considerable number of them are miscalled). The proteins were aligned with MAFFT E-INS-i (for sequences with multiple conserved domains and long gaps) with the default parameters. The alignment was curated with BMGE with a Blosum 30 similarity matrix. The Maximum Likelihood phylogeny was carried out with PhyML 3.0 with automatic model selection (LG substitution model selected). Numbers at nodes indicate aLRTs (approximate Likelihood Ratio test values).