The class Hematozoa encompasses several clinically important genera, including
Plasmodium, whose members cause the major life-threating disease malaria. Hence, a good understanding of the interrelationships of organisms from this class and reliable means for distinguishing them are of much importance. This study reports comprehensive phylogenetic and comparative analyses on protein sequences on the genomes of 28 hematozoa species to understand their interrelationships. In addition to phylogenetic trees based on two large datasets of protein sequences, detailed comparative analyses were carried out on the genomes of hematozoa species to identify novel molecular synapomorphies consisting of conserved signature indels (CSIs) in protein sequences. These studies have identified 79 CSIs that are exclusively present in specific groups of Hematozoa
/Plasmodium species, also supported by phylogenetic analysis, providing reliable means for the identification of these species groups and understanding their interrelationships. Of these CSIs, six CSIs are specifically shared by all hematozoa species, two CSIs serve to distinguish members of the order Piroplasmida, five CSIs are uniquely found in all Piroplasmida species except
B. microti and two CSIs are specific for the genus
Theileria. Additionally, we also describe 23 CSIs that are exclusively present in all genome-sequenced
Plasmodium species and two, nine, ten and eight CSIs which are specific for members of the
Plasmodium subgenera
Haemamoeba, Laverania,
Vinckeia and
Plasmodium (excluding
P. ovale and
P. malariae), respectively. Additionally, our work has identified several CSIs that support species relationships which are not evident from phylogenetic analysis. Of these CSIs, one CSI supports the ancestral nature of the avian-
Plasmodium species in comparison to the mammalian-infecting groups of
Plasmodium species, four CSIs strongly support a specific relationship of species between the subgenera
Plasmodium and
Vinckeia and three CSIs each that reliably group
P. malariae with members of the subgenus
Plasmodium and
P. ovale within the subgenus
Vinckeia, respectively. These results provide a reliable framework for understanding the evolutionary relationships among the
Plasmodium/Piroplasmida species. Further, in view of the exclusivity of the described molecular markers for the indicated groups of hematozoa species, particularly large numbers of unique characteristics that are specific for all
Plasmodium species, they provide important molecular tools for biochemical/genetic studies and for developing novel diagnostics and therapeutics for these organisms.
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