Additional file 3: of Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

Sheet 1: Accession numbers and corresponding orthogroups for all kinetoplastid species used in this analysis. Sheet 2: Accession numbers for the genes required for arginine and amino sugar metabolism in the Mollicutes. Sheet 3: The model was run on the dataset of orthologous genes (as described in the “Inference of orthogroups and construction of multiple sequence alignments” section in the “Methods”) and it was also run separately on all complete coding sequences. A complete coding sequence was considered as any coding sequence with start and stop codons whose length was divisible by 3 and longer than 30 nucleotides. This sheet shows the parameters obtained for each of the LN, MN and HN groups for both the Mollicutes and kinetoplastid parasites. Highlighted in yellow are the parameters obtained for the original two-parameter model that only considers selection acting on nitrogen content in coding sequences and mutation bias. Highlighted in green are the values obtained for the three-parameter model, which also considers selection acting on translational efficiency (tAI). The model parameters that produce the highest log likelihood values and the lowest AIC values are the best fit to the observed data. Sheet 4: Genome locations, nitrogen use and aligned sequences for Mollicutes 5S, 16S and 23S rRNA. Total nitrogen used in rRNA per 70S ribosome is given in the top left corner. Sheet 5: Genome locations, nitrogen use and aligned sequences for kinetoplastid 5.8S, 18S, 23S alpha and 23S beta rRNA. Total nitrogen used in rRNA per 80S ribosome is given in the top left corner. Sheet 6: Accession numbers for the genes required for arginine and amino sugar metabolism in the Mollicutes. (XLSX 639 kb)