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Comparative genomics of apicomplexa
Apicomplexans constitute a group of phylogenetically related protists, mostly parasites, sharing unique ultrastructural features that enable it to invade host organisms. The group includes causative agents of diseases imposing huge burden on human and animal health, such as Plasmodium falciparum (malaria – affecting ~220 million and killing ~1 million people in 2010), Toxoplasma gondii (toxoplasmosis – 3rd of the human population carrying an infection, fatal in immunocompromised individuals), Cryptosporidium parvum (Cryptosporidiosis – one of the most common waterborne diseases worldwide). However, treatment options are limited, complicated further by the growth of resistant strains. Therefore, there is an urgent need to understand the unique biology of the apicomplexans in order to develop new therapeutics.

The availability of complete and partial genomes for several apicomplexan species enables us to understand different aspects of apicomplexan biology via comparative genomics studies.

The origins of apicomplexan sequence innovation

A large-scale comparison of the protein complement in 15 apicomplexan species with standard protein sequence databases such as Uniprot, COGENT and PartiGeneDB elucidates the extent of apicomplexan sequence diversity. Around 9134 protein families were identified to be apicomplexan-specialized; with most of them being associated with individual genus or species. Strikingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Surprisingly, some families involved in housekeeping processes such as transcription and translation were significantly diverged enough to not be related by sequence homology.
Wasmuth, J., Daub, J., Peregrin-Alvarez, J.M.,Finney, C.A.M. and Parkinson, J. (2009) The origins of apicomplexan sequence innovation. Genome Research. 19:1202-1213.

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum

Apart from large-scale analyses, comparative analyses of specific genomes and specific protein families reveal the molecular basis of lineage-specific lifestyle adaptations.
Toxoplasma gondii and Neospora caninum are two closely-related tissue-dwelling parasitic apicomplexans, belonging to class Coccidia. The former has an expanded host range in vertebrates whereas the latter’s host range is restricted to cattle. Further, T. gondii relies on horizontal transmission whereas N. caninum is transmitted vertically. Comparative genomics and transcriptomics of these two species reveal a high degree of conservation of their genomes and gene expression. Surprisingly, the disparity in host range and transmission strategy seems to be influenced by a small number of gene products involved in host-parasite interaction.
Reid, A.J., Vermont, S.J., Cotton, J.A., Harris, D., Hill-Cawthorne, G.A., Könen-Waisman, S., Latham, S., Mourier, T., Norton, R., Quail, M.A., Sanders, M., Shanmugam, D., Sohal, A., Wasmuth, J.D., Brunk, B., Grigg, M.E., Howard, J.C., Parkinson, J., Roos, D.S., Trees, A.J., Berriman, M., Pain, A. and Wastling, J.M. (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens.8(3): e1002567.

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