Genome annotation and metabolic reconstruction of apicomplexan parasites

The apicomplexans are causative agents of human and animal infections including malaria, toxoplasmosis and theileriosis and have a huge economic and social impact. A number of apicomplexan genomes have been sequenced. However, the annotation of gene functions remains challenging. A semi-automatic approach was used to systematically assign genes to their functions within pathways/networks through the integration of genomic information with biochemical evidence from the literature. This method has resulted in the evidence-based annotation of metabolic functions and the development of organism specific metabolic pathways. A web database named Library of Apicomplexan Metabolic Pathways (LAMP, www.llamp.net) was developed to host the metabolic mappings for Toxoplasma gondii, Neospora caninum, Cryptosporidium and Theileria species and Babesia bovis at present. A comparative analysis of the overall metabolic capabilities of apicomplexan species showed that the metabolic adaptations has evolved for different ecological niches and led to the identification of putative drug targets. The identification of missing enzymes that are essential to complete the metabolic pathways and the identification of a subsection of these missing enzymes from raw genomes demonstrated probable inaccuracies in gene model predictions. The utilisation of T. gondii and N. caninum proteomic datasets and their mapping to alternative gene models showed regions of genes that require further refinement. The evaluation of the quality of two different gene model releases with this peptide evidence showed the importance of integration of RNA-Seq datasets in improving gene models and further improvements that can be made with proteomic datasets. A global post-translational modification (PTM) analysis was carried out for T. gondii and N. caninum via the utilisation of non-enriched proteomic datasets available for these species. This analysis identified proteins of functional importance that have undergone PTMs, particularly methylation, acetylation, phosphorylation and oxidative modifications. All these analyses helped in the improvement of gene models and functional annotation of genes from Apicomplexa genomes.