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Genome analysis is a global approach centered on a large-scale synthesis of genetic and physical mapping information and has emerged as one of the most effective tools for molecular genetics. Protozoan parasites have several common genomic features: (1) asexual or clonal growth is a normal part of the life cycle, (2) the haploid genome sizes are about the size of the smallest human chromosome, (3) the chromosomes can generally be resolved by pulsed-field gel electrophoresis (PFGE), (4) chromosome size polymorphisms among natural isolates are relatively frequent, and (5) the genomes appear to have relatively little dispersed-repetitive DNA. The trypanosomatids that include Trypanosoma and Leishmania species share some unusual properties: (1) all messenger RNAs are trans-spliced with a 5' spliced leader or miniexon 39-nucleotide sequence and (2) many genes are …