Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures. Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures

Encephalitozoon cuniculi (Microsporidia) harbours a small nuclear genome (2.9 Mbp, 11 chromosomes) in which one rDNA unit is associated with each chromosome end. However, the published genome sequence contains only 3 of the 22 expected rDNA units because of the incomplete assembly of subtelomeric contigs. We report the mapping of all duplicated segments upstream of rDNA and the analysis of major biases in nucleotide distribution. The available subtelomeric regions are found to be characterized by a few copies of eight homology blocks (EXTs) ranging in size from 3565 to 23855 kbp. Long-range PCR and sequencing data validate the junctions with rDNA, allowing the reassembly of missing areas and creation of two new EXT blocks. Several recombination sites are suggestive of translocations involving double-strand break repair. Most EXT-located CDSs (136) are ascribed to four multigene families that may be crucial for parasite adaptability. Modelling of DNA denaturation (GeneFizz server) supports a relationship between recombination sites and open-closed transitions. Two-dimensional representation of GC and AT skews reveals nearly monotonic functions for EXT and rDNA regions. Similar topologies are detected in the subtelomeres of Guillardia theta, a eukaryotic endosymbiont having a miniaturized genome that also retains one rDNA unit at each chromosome end.