Figure 2

Prediction of taxonomic groups from codon usage profiles. (A) Distribution of predicted taxonomic groups based on GC-normalized RSCU profiles. Codon usage profiles of P. pacificus genes were compared to the average genomewide profiles of 71 species and assigned to the species with the closest Euclidean distance in profiles. (B) Enrichment of predicted taxonomic groups for P. pacificus orphans with respect to all genes. The strongest enrichment in predicted taxonomic groups is observed for bacteria, however due to the small number of bacteria predictions in general, it is not the most significant enrichment and might be a side effect of the depletion in predicted nematode codon profiles. In contrast, the most significant bias is observed for genes with predicted insect-like codon usage. (C) Relative distance to Drosophila melanogaster GC-normalized RSCU profile with respect to distances to P. pacificus and Aspergillus nidulans. In comparison to P. pacificus genes with homologs in other nematodes, both classes of HGT candidates show a strongly reduced distance to the Drosophila melanogaster profile.