Analysis of reassigned stop codons distribution in B. nonstop proteins

Codon usage
To compare the usage of reassigned stop codons in the nuclear-encoded mitochondrial proteins and non-mitochondrial proteins of Blastocrithidia, we needed to define mitochondrial proteins of Blastocrithidia. We decided to rely on the protein homologues from T. brucei. As mitochondrial dataset for T. brucei we used the set of the proteins imported into the mitochondrion (importome) obtained by Peikert and colleagues (Peikert et al., 2017).
For this analysis, we took only genes that had a single ortholog in Blastocrithidia and a single orthologue in T. brucei. There were 4,561 of these genes. We defined as mitochondrial those proteins of B. nonstop that had an importome orthologue in T. brucei. There were 892 of such proteins. The rest 3’669 were defined as non-mitochondrial. Then for each gene we calculated relative abundance of the reassigned stop codons (stop share) - a proportion of reassigned stop codons divided by the total number of codons encoding glutamate and tryptophan. Relative protein abundance was calculated as the number of individual peptides coming from a protein divided by the maximum number of peptides coming from one protein.