Physical map of a 2 Mb chromosome of the intestinal protozoan parasite Giardia duodenalis

The protozoan parasite, Giardia duodenalis, is regarded as the most primitive eukaryote. The two apparently identical nuclei presumably carry the same chromosomes but the number of different chromosomes in the organism is unknown. A genome map of G. duodenalis is required to resolve this issue and mapping studies were initiated using chromosome 5. This chromosome was estimated to be approximately 2 Mb when Giardia chromosomes were separated by contour-clamped homogeneous electric field gel electrophoresis. A plasmid library of chromosome 5-specific DNA sequences was constructed from gel-extracted chromosome 5 and selected probes were used as markers to identify NoN DNA segments derived from chromosome 5. Fifty-nine unique copy markers were used to identify thirteen NoN segments which ranged in size from 47 kb to 400 kb. The sum of the NotI segments was 1.78 Mb which indicated that most, if not all, of the chromosome was accounted for and that chromosome band 5 of the cloned line WB-1B, used in this study comprised only one chromosome type. The NoN segments were ordered on the map by comparison of hybridization patterns of the markers with partial NotI cleavages of whole chromosomes. Chromosome rearrangements occur readily in Giardia, and in two drug-resistant lines selected for resistance to different drugs, partial conservative duplications of chromosome 5 were observed in addition to the original, full length chromosome 5. Both duplications retained the central region of chromosome 5 but were deleted at different termini resulting in one duplication of 1.5 Mb and the other of 1.3 Mb. The duplicated chromosomes which appeared to be in lower copy number than the parent chromosome gave rise to a stable aneuploid organism. Chromosome maps of organisms with weak genetic databases, such as Giardia, will be extremely useful for determining genome organisation and plasticity.