Evolutionary Pressures and Codon Bias in Low Complexity Regions of Plasmodia Parasites

One of the most debated topics in Evolutionary Biology concerns Low Complexity Regions of P. falciparum, the causative agent of the most virulent and deadly form of human malaria. In this work, we analysed the proteome of 22 plasmodium species including P. falciparum. SEG predicts that proteins containing Low Complexity Regions turn out to be longer than those which are predicted to be completely complex (without Low Complexity Regions). Moreover, using some well-known bioinformatics tools such as the Effective Number of Codons, the Pr2 and a new index that we have called SPI, we have noticed how proteins that embed Low Complexity Regions are under lower selective pressure than those that do not present this type of locus. By applying the Relative Synonymous Codon Usage and other tools developed ad hoc for this study, we note, instead, how the Low Complexity Regions appear to have a non-neutral codon bias with respect to the host proteins.