Status of protozoan genome analysis: trypanosomatids

The three trypanosomatid genome projects have employed common strategies wh ich include: analysis of pulsed-field gel electrophoretic chromosomal karyo types; physical mapping using big DNA (cosmid, pacmid P1, bacterial artific ial chromosome, yeast artificial chromosome) libraries; partial cDNA sequen ce analysis to develop sets of expressed sequence tags (ESTs) for gene disc overy and use as markers in physical mapping; genomic sequencing; dissemina tion of information through development of web-sites and ACeDB-based fully integrated databases; and establishment of functional genomics programmes t o maximize useful application of genome data. Highlights of the projects to date have been the demonstration that, despite extensive chromosomal size polymorphisms for diploid homologues within Africa trypanosomes, T. cruzi o r Leishmania, the physical linkage groups for markers on each chromosome ar e retained across all isolates/species studied within each group. For Afric an trypanosomes, detailed analysis of chromosome 1 has demonstrated that re petitive sequences and the two retroposon-like elements RIME and INGI are l ocalized to a defined region at one end of the chromosome, with the bulk of the central region of the chromosome containing genes coding for expressed proteins. Comparative mapping shows that, although subtelomeric changes ac count for a large proportion of the polymorphism in chromosome size in Afri can trypanosomes, there are significant expansions and contractions in regi ons across the entire chromosome. The highlight of the genomic sequencing p rojects has been the demonstration of just 2 putative transcriptional units of chromosome 1 of Leishmania major, extending on opposite strands from a point in the central region of the chromosome. A similar observation made o n 93.4 kb of contiguous sequence for T. cruzi chromosome 3 suggests the pre sence of promoter and regulatory elements at the junctions of large polycis tronic transcriptional units. All data obtained from the genome projects ar e made available through the public domain, which has prompted changing phi losophies in how we approach analysis of the biology of these organisms, an d strategies that we can employ now in the search for new therapies and vac cines.