Genome and transcriptome studies of the protozoan parasites Trypanosoma cruzi and Giardia intestinalis

Abstract: Trypanosoma cruzi and Giardia intestinalis are two human pathogens and protozoan parasites responsible for the diseases Chagas disease and giardiasis, respectively. Both diseases cause su ering and illness in several million individuals. The former disease occurs primarily in South America and Central America, and the latter disease occurs worldwide. Current therapeutics are toxic and lack e cacy, and potential vaccines are far from the market. Increased knowledge about the biology of these parasites is essential for drug and vaccine development, and new diagnostic tests. In this thesis, high-throughput sequencing was applied together with extensive bioinformatic analyses to yield insights into the biology and evolution of Trypanosoma cruzi and Giardia in- testinalis. Bioinformatics analysis of DNA and RNA sequences was performed to identify features that may be of importance for parasite biology and functional characterization. This thesis is based on ve papers (i -v). Paper i and ii describe comparative genome studies of three distinct genotypes of Giardia in- testinalis (A, B and E). The genome-wide divergence between A and B was 23% and 13% between A and E. 4557 groups of three-way orthologs were de ned across the three genomes. 5 to 38 genotype-speci c genes were identi ed, along with genomic rearrangements. Genes encoding surface antigens, vsps, had undergone extensive diversi cation in the three genotypes. Several bacterial gene transfers were identi ed, one of which encoded an acetyltransferase protein in the E genotype. Paper iii describes a genome comparison of the human infecting Trypanosoma cruzi with the bat-restricted subspecies Trypanosoma cruzi marinkellei. The human infecting parasite had an 11% larger genome, and was found to have expanded repertoires of sequences related to surface antigens. The two parasites had a shared `core' gene complement. One recent horizontal gene transfer was identi ed in T. c. marinkellei, representing a eukaryoteto- eukaryote transfer from a photosynthesizing organism. Paper iv describes the repertoire of small non-coding RNAs in Trypanosoma cruzi epimastigotes. Sequenced small RNAs were in the size range 16 to 61 nucleotides, and the majority were derived from transfer RNAs and other non-coding RNAs. 92 novel transcribed loci were identi ed in the genome, 79 of which were without similarity to known RNA classes. One population of small RNAs were derived from protein-coding genes. Paper v describes transcriptome analysis using paired-end RNA-Seq of three distinct genotypes of Giardia intestinalis (A, B and E). Gene expression pro les recapitulated the known phylogeny of the examined genotypes, and 61 to 176 genes were di erentially expressed. 49,027 distinct polyadenylation sites were mapped and compared, and the median 30UTR length was 80 nucleotides (A). One 36-nt novel intron was identi ed and the previously reported introns (5) were con rmed.