Encephalitozoon cuniculi (microspora) genome:: physical map and evidence for telomere-associated rDNA units on all chromosomes

A restriction map of the 2.8-Mb genome of the unicellular eukaryote Encephalitozoon cuniculi (phylum Microspora), a mammal-infecting intracellular parasite, has been constructed using two restriction enzymes with 6 bp recognition sites (BssHII and MIuI), The fragments resulting from either single digestions of the whole molecular karyotype or double digestions of 11 individual chromosomes have been separated by two-dimensional pulsed field gel electrophoresis (2D-PFGE) procedures, The average distance between successive restriction sites is similar to 19 kb, The terminal regions of the chromosomes show a common pattern covering similar to 15 kb and including one 16S-23S rDNA unit. Results of hybridisation and molecular combing experiments indicate a palindromic-like orientation of the two subtelomeric rDNA copies on each chromosome. We have also located 67 DNA markers (clones from a partial E. cuniculi genomic library) by hybridisation to restriction fragments. Partial or complete sequencing has revealed homologies with known protein-coding genes for 32 of these clones. Evidence for two homologous chromosomes ill, with a size difference (3 kb) related to a subtelomeric deletion/insertion event, argues for diploidy of E,cuniculi, The physical map should be useful for both the whole genome sequencing project and studies on genome plasticity of this widespread parasite.