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 Encepha litozoon cuniculi (phylum Microspora), a mammal-infecting intracellular par asite, has been constructed using two restriction enzymes with 6 bp recogni tion sites (BssHII and MIuI), The fragments resulting from either single di gestions of the whole molecular karyotype or double digestions of 11 indivi dual chromosomes have been separated by two-dimensional pulsed field gel el ectrophoresis (2D-PFGE) procedures, The average distance between successive restriction sites is similar to 19 kb, The terminal regions of the chromos omes show a common pattern covering similar to 15 kb and including one 16S- 23S rDNA unit. Results of hybridisation and molecular combing experiments i ndicate a palindromic-like orientation of the two subtelomeric rDNA copies on each chromosome. We have also located 67 DNA markers (clones from a part ial 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 chromosome s ill, with a size difference (3 kb) related to a subtelomeric deletion/ins ertion 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.