Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium

Unlike other eukaryotes, malaria parasites in the genus Plasmodium have structurally and functionally different paralogous copies of the cytosolic (cyto-) SSU rRNA (18S rRNA) gene that are expressed at different developmental stages. In P. falciparum, P. vivax, and P. berghei, A-type cyto-SSU rRNA is expressed in asexual stage, while S-type in sporozoite stage. A third type (O-type) has been described in P. vivax. It is expressed only in oocyst stage in the mosquito. Recently, it has been shown that the maintenance of heterogeneous cyto-SSU rRNAs in Plasmodium can be modeled as a birth-and-death process under strong purifying selection [Rooney, A.P., 2004. Mechanisms underlying the evolution and maintenance of functionally heterogeneous 18S rRNA genes in Apicomplexans. Mol. Biol. Evol. 21, 1704–1711]. In this study, we performed detailed phylogenetic analyses of Plasmodium cyto-SSU rRNAs with special emphasis on the evolution of multi-copy genes in simian Plasmodium species. We sequenced paralogous copies of the cyto-SSU rRNA genes from an African simian Plasmodium species, P. gonderi, and Asian simian Plasmodium species, P. fragile, P. coatneyi, P. inui, P. hylobati, P. fieldi, P. simiovale, and P. cynomolgi. Interestingly, all Asian simian Plasmodium species have a single S-type-like gene and several A-type-like genes. Alignment analysis demonstrated for the first time that an approximately 50-residue insertion in the V7 variable region near the stem 43 is shared exclusively by the S-type-like sequences of the Asian simian Plasmodium species and the S- and O-type sequences of P. vivax. We comprehensively analyzed all cyto-SSU rRNA sequences of the genus Plasmodium currently available in the database. Phylogenetic analyses of all publicly available cyto-SSU rRNA sequences for the genus Plasmodium clearly demonstrated that gene duplication events giving rise to A- and S-type-like sequences took place independently at least three times in the Plasmodium evolution, supporting the hypothesis that these genes evolve according to a birth-and-death model.