Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)

Graduate Group


First Advisor

David S. Roos


This dissertation exploits phylogenomic approaches to identify genes and gene families likely to be important in the biology of apicomplexan parasites, including Plasmodium (the causative agent of malaria) and Toxoplasma (a leading source of congenital neurological birth defects, and a prominent opportunistic infection in immunosuppressed individuals). In particular, we have explored the significance of lateral gene transfer and gene duplication as sources of evolutionary novelty . Genomic-scale phylogenetic tree comparison identifies surprisingly extensive lateral gene transfer (LGT), including plant-like genes presumably acquired from the algal source of the apicomplexan plastid (apicoplast), and animal-like genes that may have been acquired from these parasites’ host species. Studies on apicomplexan-specific expanded gene families indicate that kinases are a probable source of functional innovation. The T. gondii kinome displays previously under-appreciated diversity in parasite-specific secreted kinases associated with the rhoptry organelles required for host cell invasion. Evolutionary analysis points to the importance of this ‘ROPK’ family, and functional genomics datasets were employed to prioritize family members for further investigation, including subcellular localization and overexpression in transgenic parasites. Transcriptional profiling of host-cell responses to infection, coupled with functional clustering, reveals pathways likely to be regulated by the parasite, and a role for ROP38 in controlling this process. Our studies highlight the potential of combining phylogenetics with genome-scale analysis and experimental manipulation to elucidate biological function; similar strategies should be generally useful in integrating the diverse range of genomic-scale datasets that increasingly characterizes modern biomedical research.

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Additional Files

SuplementaryFigure4.1.ppt (1331 kB)
Supplementary figure 4.1. ROPK Subcellular localization

SuplementaryFigure4.2.ppt (375 kB)
Supplementary Figure 4.2 ROPK Multiple Sequence Alignment

SuplementaryTable2.1.xls (163 kB)
Supplementary Table 2.1 Distribution of connectivity values and size for the test data set (79 ortholog groups).

SuplementaryTable3.1.xls (22 kB)
Supplementary Table 3.1. List of species and species abbreviations used.

SuplementaryTable3.2.xls (98 kB)
Supplementary Table 3.2 LGT results for manual curation of enzymes

SuplementaryTable3.3.xls (493 kB)
Supplementary Table 3.3. Ranked list of LGT candidates from LGTsmart

SuplementaryTable4.1.xls (114 kB)
Supplementary Table 4.1. The T. gondii kinome: kinases and pseudokinases by group

SuplementaryTable4.2.xls (57 kB)
Supplementary Table 4.2. The ROP-K family

SuplementaryTable4.3.xls (1948 kB)
Supplementary Table 4.3. Expression profile of ROP-K transgenic lines

SuplementaryTable4.4.xls (11843 kB)
Supplementary Table 4.4. Host-gene expression in response to infection

SuplementaryTable4.5.xls (1589 kB)
Supplementary Table 4.5. Functional annotation of transcripts altered by infection