Delineation of the Genera Haemoproteus and Plasmodium Using RNA-Seq and Multi-gene Phylogenetics

Abstract

Members of the order Haemosporida are protist parasites that infect mammals, reptiles and birds. This group includes the causal agents of malaria, Plasmodium parasites, the genera Leucocytozoon and Fallisia, as well as the species rich genus Haemoproteus with its two subgenera Haemoproteus and Parahaemoproteus. Some species of Haemoproteus cause severe disease in avian hosts, and these parasites display high levels of diversity worldwide. This diversity emphasizes the need for accurate evolutionary information. Most molecular studies of wildlife haemosporidians use a bar coding approach by sequencing a fragment of the mitochondrial cytochrome b gene. This method is efficient at differentiating parasite lineages but insufficient for accurate phylogenetic inferences in highly diverse taxa such as haemosporidians. Recent studies have utilized multiple mitochondrial genes (cyt b, cox1 and cox3), sometimes combined with a few apicoplast and nuclear genes. These studies have been highly successful with one notable exception: the evolutionary relationships of the genus Haemoproteus remain unresolved. Here we describe the transcriptome of Haemoproteus columbae and investigate its phylogenetic position recovered from a multi-gene dataset (600 genes). This genomic approach restricts the taxon sampling to 18 species of apicomplexan parasites. We employed Bayesian inference and maximum likelihood methods of phylogenetic analyses and found H. columbae and a representative from the subgenus Parahaemoproteus to be sister taxa. This result strengthens the hypothesis of genus Haemoproteus being monophyletic; however, resolving this question will require sequences of orthologs from, in particular, representatives of Leucocytozoon species.

Keys to the avian Haemoproteus parasites (Haemosporida, Haemoproteidae)

“…Thus, morphologically similar parasites in birds belonging to different orders are different species in most cases. This conclusion was confirmed by molecular data [ 7 , 9 , 11 , 13 ]. Due to vertebrate host specificity and the resulting restriction of parasite distributions by bird orders, the natural host range of haemosporidians remains helpful in species identification.…”

“…Molecular phylogenetic data show that Haemoproteus parasites (Haemoproteidae) are a sister group to malaria agents of the genus Plasmodium (Plasmodiidae) [ 8 , 9 , 11 ]. Haemosporidians of both these genera do not digest haemoglobin completely, resulting in the accumulation of residual pigment (haemozoin) in their blood stages [ 1 – 3 ].…”

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys

“…However, we did find fragmentary sequences with significant sequence similarity to RBPs from malaria parasites with avian hosts in transcriptome assemblies of Leucocytozoon buteonis [ 22 ] and Hae . columbae [ 23 ] ( S11 Fig ). Also missing from this cluster was Cdpk5 , a kinase that regulates parasite egress from red cells [ 24 ].…”

“…A transcriptome assembly of Haemoproteus columbae [ 23 ] was downloaded from GenBank (GenBank ID GGWD00000000.1). Illumina MiSeq reads of Leucocytozoon and its host Buteo buteo were downloaded from the European Nucleotide Archive (study PRJEB5722).…”

“… (A) Alignment of the translation of a sequence (GGWD01016989.1) from Haemoproteus columbae transcriptome assembly (GenBank: GGWD00000000.1) [ 23 ] with Plasmodium reticulocyte-binding proteins (RBPs) from PlasmoDB [ 115 ]. The alignment has been cropped to the length of the Haemoproteus columbae sequence.…”