Supplementary Dataset 1. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

Schematic visualization of the evolutionary changes on KEGG pathways analyzed in this work. Each file corresponds to one pathway, where the symbols are equivalent to those listed in Supplementary Figure 4. The scores of each enzyme are represented by the size of the dot (see legend), and they can be interactively added/removed. Each symbol represents a gene which, upon hover with the cursor, displays an informative box. This provides many lines of evolutionary information: 1) Gene name, one of the kegg orthologs (KOs) and name of the enzyme, KO for which the mapping was established. 2) Evolutionary processes found in this gene, including duplication (duplicated_in_any), positive selection (possel), mitochondrial retargeting (mito_retargeting), loss (lost_in_any), co-loss (co-lost_in_, meaning that this gene is lost together with orthologs of the other CI loss events), orphan and the intersections between all these categories. For orphan genes, the top 5 blastp hits to the latest version of the trembl database are shown, which should help to understand if they are true orphans. 3) The codon adaptation index (CAI) of the gene and the one of the orthologs of the sister CI+ species (CI+ orthologs). 4) The results of subcellular localization prediction (performed using deeploc) where, for each location with a p > 0.1, the probability of localization (pLoc) of the gene and the CI+ orthologs are shown. 5) The interproscan annotations of the genes, where each gene is one annotation. 6) The InterProScan annotation of all CI+ orthologs, where each line corresponds to one ortholog, and the annotations are delimited by “|”.