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.
Highlights
The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes
Mosaic organisation of chromosome ends The two ends of each chromosome (Σ) of E. cuniculi were designated as Σα and Σβ, referring to the 5’ and 3’ ends of the Watson strand of the sequence deposited in the database, respectively
Our analysis revealed that the available sequence of the subtelomeric regions is incomplete for the following three reasons: (i) the rDNAcontaining repeat is only found on both ends of chromosome I and on IVα extremity whereas previously reported physical mapping data indicated that each subtelomere includes the transcription unit of Ribosomal Ribonucleic acid (rRNA) (rDNA) unit [6]; (ii) no genes belonging to gene families known to associate with chromosome ends were detected on IIIβ and IXα, and (iii) short duplicated sequences at far extremities are due to artificial truncations of subtelomeric specific repeats (Additional file 1: Figure S2B)
Summary
The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. 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. The ~ 2.9 Mbp nuclear genome of E. cuniculi consists of 11 chromosomes ranging in size between 217 and 315 kbp [5]. Three E. cuniculi strains (I, II and III) have so far been identified on the basis of their immunological profile as well as by molecular analyses based on the presence of a variable number of GTTT repeats within the unique rDNA internal transcribed spacer separating the two rRNA-coding regions [7]. Chromosomal length polymorphisms (CLPs) were found to be in the form of insertion-deletion events (Indels) over 3–10 kbp in size, occurring within transition zones between rDNA units and chromosome cores [10]
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