Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: Compositional constraints and translational selection

We have analyzed the patterns of synonymous codon preferences of the nuclea r genes of Plasmodium falciparum, a unicellular parasite characterized by a n extremely GC-poor genome. When all genes are considered, codon usage is s trongly biased toward A and T in third codon positions, as expected, but mu ltivariate statistical analysis detects a major trend among genes. At one e nd genes display codon choices determined mainly by the extreme genome comp osition of this parasite, and very probably their expression level is low. At the other end a few genes exhibit an increased relative usage of a parti cular subset of codons, many of which are C-ending. Since the majority of t hese few genes is putatively highly expressed, we postulate that the increa sed C-ending codons are translationally optimal. In conclusion, while codon usage of the majority of P. falciparum genes is determined mainly by compo sitional constraints, a small number of genes exhibit translational selecti on.