EVOLUTION OF CODON USAGE AND BASE CONTENTS IN KINETOPLASTID PROTOZOANS

In this study we analyze and compare the trends in codon usage in five representative species of kinetoplastid protozoans (Crithidia fascicu lata, Leishmania donovani, L. major, Trypanosoma cruzi and T. brucei), with the purpose of investigating the processes underlying these tren ds. A principal component analysis shows that the G + C content at the third codon position represents the main source of codon-usage variat ion, both within species (among genes) and among species. The non-Tryp anosoma species exhibit narrow distributions in codon usage, while bot h Trypanosoma species present large within-species heterogeneity. The three non-Trypanosoma species have very similar codon-usage preference s. These codon preferences are also shared by the highly expressed gen es of T. cruzi and to a lesser degree by those of T. brucei. This lead s to the conclusion that the codon preferences shared by these species are the ancestral ones in the kinetoplastids. On the other hand, the study of noncoding sequences shows that Trypanosoma species exhibit mu tational biases toward A + T richness, while the non-Trypanosoma speci es present mutational pressure in the opposite direction. These data t aken together allow us to infer the origin of the different codon-usag e distributions observed in the five species studied. In C. fasciculat a and Leishmania, both mutational biases and (translational) selection pull toward G + C richness, resulting in a narrow distribution. In Tr ypanosoma species the mutational pressure toward A + T richness produc ed a shift in their genomes that differentially affected coding and no ncoding sequences. The effect of these pressures on the third codon po sition of genes seems to have been inversely proportional to the level of gene expression.