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

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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.

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Acknowledgements

This work was supported by Research Council of Lithuania (Grant MIP-045/2015). This study was also supported by the grant to RNMS, NIH 1SC3GM118210-01A1. The authors would like to thank Elvin J. Lauron, Bradley Bowser and Dr. Frank Cipriano for helping in planning rna-seq and project logistics. We are grateful to Dr. Greg Spicer, Andrew Ontano, Dr. Emily Jane McTavish and Trent Liu for assistance on phylogenetic and scripting advisement.

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Authors and Affiliations

  1. Department of Biology, San Francisco State University, 1700 Holloway Ave, San Francisco, CA, 94132, USA

    Jasper Toscani Field, Josh Weinberg & Ravinder N. M. Sehgal

  2. Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden

    Staffan Bensch

  3. Sede Bogotá, Facultad de Ciencias, Departamento de Biología, Grupo de Investigación Caracterización genética e inmunología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, 111321, Colombia

    Nubia E. Matta

  4. Nature Research Centre, Akademijos 2, 08412, Vilnius 21, Lithuania

    Gediminas Valkiūnas

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  1. Jasper Toscani Field
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Correspondence to Jasper Toscani Field.

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Accession numbers: H. columbae raw reads GenBank ID: SAMN06899305. H. columbae transcriptome assembly GenBank ID: GGWD00000000.

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Toscani Field, J., Weinberg, J., Bensch, S. et al. Delineation of the Genera Haemoproteus and Plasmodium Using RNA-Seq and Multi-gene Phylogenetics. J Mol Evol 86, 646–654 (2018). https://doi.org/10.1007/s00239-018-9875-3

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