Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signaturesReport as inadecuate




Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 17:34

First Online: 07 January 2016Received: 28 January 2015Accepted: 11 September 2015DOI: 10.1186-s12864-015-1920-7

Cite this article as: Dia, N., Lavie, L., Faye, N. et al. BMC Genomics 2016 17: 34. doi:10.1186-s12864-015-1920-7

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.

KeywordsMicrosporidia Encephalitozoon cuniculi Subtelomere Chromosome ends Recombination Multigene family AbbreviationsrDNAtranscription unit of rRNA

rRNARibosomal Ribonucleic acid

PCRPolymerase Chain Reaction

BLASTBasic Local Alignment Search Tool

CDSCoding region sequence

PFGEPulsed Field Gel Electrophoresis

ORFOpen Reading Frame

NADNicotinamid Adenine Dinucleotide

CLPChromosome Length Polymorphism

DSBRDouble Strand Break Repair

BIRBreak Induced Replication

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1920-7 contains supplementary material, which is available to authorized users.

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Author: Ndongo Dia - Laurence Lavie - Ngor Faye - Guy Méténier - Edouard Yeramian - Christophe Duroure - Bhen S. Toguebaye - Rog

Source: https://link.springer.com/







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