Insights into the genome sequence of a free-living kinetoplastid: Bodo saltans (kinetoplastida: Euglenozoa)

Abstract

Background: Bodo saltans is a free-living kinetoplastid and among the closest relatives of the trypanosomatid parasites, which cause such human diseases as African sleeping sickness, leishmaniasis and Chagas disease. A B. saltans genome sequence will provide a free-living comparison with parasitic genomes necessary for comparative analyses of existing and future trypanosomatid genomic resources. Various coding regions were sequenced to provide a preliminary insight into the bodonid genome sequence, relative to trypanosomatid sequences. Results: 0.4 Mbpof B. saltans genome was sequenced from 12 distinct regions and contained 178 coding sequences. As in trypanosomatids, introns were absent and %GC was elevated in coding regions, greatly assisting in gene finding. In the regions studied, roughly 60% of all genes had homologs in trypanosomatids, while 28% were Bodo-specific. Intergenic sequences were typically short, resulting in higher gene density than in trypanosomatids. Although synteny was typically conserved for those genes with trypanosomatid homologs, strict colinearity was rarely observed because gene order was regularly disrupted by Bodo-specific genes. Conclusion: The B. saltans genome contains both sequences homologous to trypanosomatids and sequences never seen before. Structural similarities suggest that its assembly should be solvable, and, although de novo assembly will be necessary, existing trypanosomatid projects will provide some guide to annotation. A complete genome sequence will provide an effective ancestral model for understanding the shared and derived features of known trypanosomatid genomes, but it will also identify those kinetoplastid genome features lost during the evolution of parasitism. © 2008 Jackson et al; licensee BioMed Central Ltd.