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

Abstract

BackgroundThe microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion.ResultsHere we report the first complete assembly of E. cuniculi chromosome ends, and describe a novel mosaic structure of segmental duplications (EXT repeats) in these regions. EXT repeats range in size between 3.5 and 23.8 kbp and contain four multigene families encoding membrane associated proteins. Twenty-one recombination sites were identified in the sub-terminal region of E. cuniculi chromosomes. Our analysis suggests that these sites contribute to the diversity of chromosome ends organization through Double Strand Break repair mechanisms. The region containing EXT repeats at chromosome extremities can be differentiated based on gene composition, GC content, recombination sites density and chromosome landscape.ConclusionTogether this study provides the complete structure of the chromosome ends of E. cuniculi GB-M1, and identifies important factors, which could play a major role in parasite diversity and host-parasite interactions. Comparison with other eukaryotic genomes suggests that terminal regions could be distinguished precisely based on gene content, genetic instability and base composition biais. The diversity of processes assciated with chromosome extremities and their biological consequences, as they are presented in the present study, emphasize the fact that great effort will be necessary in the future to characterize more carefully these regions during whole genome sequencing efforts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1920-7) contains supplementary material, which is available to authorized users.

Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species

“…The InterAE, B, C and D predicted proteins accounted for a total of 50.0, 35.5 and 32.4% of the E. intestinalis , E. hellem and E. cuniculi predicted subtelomere ORFs, respectively, and several of the repeated InterC and InterD proteins appeared unique to E. hellem and E. intestinalis , suggesting that their genes were duplicated post-speciation (Table S 3 ). Albeit putative functions could not be inferred for these proteins, predictive folding revealed that members of the InterC and InterD families harbor alpha-helical structures common to transmembrane proteins, congruent with previous observations [ 9 ], and corroborated by deep-learning inferences based on sequence data (Fig. 3 ).…”

“…Of these, only 34.5% (60/174) of the ORFs predicted in the E. intestinalis subtelomeres were found shared with both E. hellem and E. cuniculi , many of which as part of large repetitive families. E. cuniculi was previously shown to harbor repetitive gene families known as interAE , interB , interC and interD in its subtelomeres [ 9 , 32 ], and those were found in all three Encephalitozoon species, albeit in different copy numbers. The InterAE, B, C and D predicted proteins accounted for a total of 50.0, 35.5 and 32.4% of the E. intestinalis , E. hellem and E. cuniculi predicted subtelomere ORFs, respectively, and several of the repeated InterC and InterD proteins appeared unique to E. hellem and E. intestinalis , suggesting that their genes were duplicated post-speciation (Table S 3 ).…”

“…In a previous study, Dia and colleagues suggested that the subtelomeres in Encephalitozoon genomes likely serve as constitutive heterochromatin loci given their overall low coding density and flanking by rRNA genes [ 9 ]. Our DNA methylation results are congruent with this hypothesis, with the subtelomeres in Encephalitozoon species showing intermediate levels of DNA methylation between the hypomethylated chromosomes cores — i.e.…”

“…Chromosome cores in Encephalitozoon spp. were hereby defined as the regions encompassing the center of all orthologous chromosomes, whose GC-contents decrease from center to edges [ 6 , 69 ], the latter of which are flanked by abrupt shifts in GC contents [ 9 ]. Subtelomeres were defined as the regions starting from the rRNA genes to the chromosome cores.…”

“…[ 3 ]. As both paradigms of genome reduction in eukaryotes and human-infecting pathogens, the latter species garnered much interest, with investigations of select representative Encephalitozoon genomes yielding strong insights about their metabolic capabilities and potential for harm [ 6 – 9 ]. However, because no Encephalitozoon genome has been sequenced from telomere-to-telomere and since little is known about their DNA methylation, our knowledge of the genetic and epigenetic architectures of these species is incomplete.…”