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Exploring the Genomes of Pathogenic Protozoans

Many parasitic protozoan genomes are relatively small, ranging from approximately 9 Mbp in Theileria and Cryptosporidium to upwards of 170 Mbp in Trichomonas vaginalis (Table 19.2), thus facilitating sequencing efforts of multiple new organisms. In concert with knowledge of complete genome sequences, gene expression profiling has emerged as an important tool to study gene function in genetically intractable organisms and has transformed the traditional "gene-by-gene" analyses originating from functional cloning methodologies. While genome sequence information itself contains considerable biological significance, and therefore data concerning DNA content, gene organization, and chromosomal

19.1 Exploring the Genomes of Pathogenic Protozoans 419

composition has informative appeal, the definition of functional pathways using bioinformatics tools (e.g., Basic Local Alignment Search Tool (BLAST)), micro-arrays, proteomics, and confirmation of function via gene disruption and transfec-tion of experimental chimeras will have a dramatic impact on exploring parasite biology. The further challenge, however, will be the translation of this knowledge into alleviation of disease.

Table 19.2 Genome sizes of parasitic protists.

Parasite

Genome size

Number of chromosomes

Cryptosporidium parvum

9 Mbp

8 chromosomes

Theileria annulata

10 Mbp

4 chromosomes

Giardia lamblia

12 Mbp

5 chromosomes

Entamoeba histolytica

20 Mbp

14 chromosomes

Plasmodium falciparum

23 Mbp

14 chromosomes

Leishmania major

34 Mbp

36 chromosomes

Trypanosoma cruzi

40 Mbp

Unknown

Eimeria tenella

60 Mbp

14 chromosomes

Toxoplasma gondii

estimated 80 Mbp

11 chromosomes

Trichomonas vaginalis

estimated 170 Mbp

6 chromosomes

To facilitate data dissemination and utilization, most publicly funded genome sequencing efforts, as well as projects generating expressed sequence tags (EST) and gene-survey sequence tags (GSS) sequencing, provide sequence download sites for real-time-generated data, either at their own website or via GenBank (Table 19.1). Additionally, web-based project sites typically post periodic summaries of significant similarity (BLAST) hits between their data and GenBank databases, and provide the capacity for web-based BLAST searches of their sequences to facilitate the identification of genes and gene discovery. For example, the genome sequence data for Plasmodium malaria parasites is presented on a website, http://www.PlasmoDB.org [6-8], that maintains data from several Plasmodium species. In addition to BLAST search engines, the site also permits gene retrieval via text-based searches, gene predictions, microsatellite marker mapping, ePCR, and searches based upon gene features or user-defined motifs. Similar databases for other parasitic protists, e.g., http://www.ToxoDB.org [9], http://TcruziDB.org [10], and http://CryptoDB.org [11], are additional valuable resources (Table 19.1). A comparative genome database, ApiDots (www.cbil.upenn.edu/apidots/), provides integrated access to publicly available mRNA/EST sequences and was con structed for the systematic approach of apicomplexan genome analysis [12,13]. The database currently incorporates ESTs from several parasite species of clinical and/or veterinary interest, including Eimeria tenella, Neospora caninum, Plasmodium falciparum, Sarcocystis neurona, Gregarina niphandrodes, and Toxoplasma gondii. Additional integrated parasite databases are provided by the Wellcome Trust Sanger Institute and the Institute for Genomic Research (TIGR; for web addresses see Table 19.1).

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