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Genome analysis is a global approach centered around a large-scale synthesis of genetic and physical mapping information and has emerged as one of the most effective tools for molecular genetics. The positional cloning of genes, identification of new loci via genetic/physical linkage, and procurement of chromosome structural data are all greatly facilitated by methods developed for this kind of research. The majority of molecular techniques generally applicable to genome analysis have been described in detail elsewhere, but each species has unique genomic characteristics which can be exploited by the modification of existing protocols and by the development of new methods.

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 (50 Mb);(3) the chromosomes can generally be resolved by pulsed-field gel electrophoresis (PFGE);(4) chromosome size polymorphisms between natural isolates are relatively frequent; and (5) the genomes appear to have relatively little dispersed-repetitive DNA. The trypanosomatids, which include Trypanosoma and Leishmania species, share some unusual properties:(1) all mRNAs are trans-spliced with a 5′" spliced leader" or" miniexon" 39-nucleotide sequence, and (2) many genes are polycistronically transcribed and may exist as tandem arrays. Some of these characteristics can be used to tailor methods specifically for the analysis of protozoan parasite genomes. This chapter describes how the ability to separate whole chromosomes by gel electrophoresis …