title: Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  Here 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.
  
  
  CONCLUSIONS
  Together 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.
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, B.P. 220, Dakar, Sénégal. ndia@pasteur.sn.
authors.forename: Ndongo
authors.initials: N
authors.lastname: Dia
authors.affiliation: Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, UMR 6023, CNRS, 63177, Aubière, France. laurence.lavie@wanadoo.fr.
authors.forename: Laurence
authors.initials: L
authors.lastname: Lavie
authors.affiliation: Laboratoire de Parasitologie Générale, Département de Biologie Animale, Faculté des Sciences et Technologies, Université Cheikh Anta Diop, Dakar, Sénégal. nfaye2002@yahoo.fr.
authors.forename: Ngor
authors.initials: N
authors.lastname: Faye
authors.affiliation: Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, UMR 6023, CNRS, 63177, Aubière, France. guymtnr@gmail.com.
authors.forename: Guy
authors.initials: G
authors.lastname: Méténier
authors.affiliation: Unité de Bioinformatique Structurale, UMR 3528 CNRS, Institut Pasteur, 25-28, rue du Dr Roux, 75015, Paris, France. yeramian@pasteur.fr.
authors.forename: Edouard
authors.initials: E
authors.lastname: Yeramian
authors.affiliation: Laboratoire de Météorologie Physique, OPGC UMR 6016 CNRS-Université Blaise Pascal, 24 Avenue des Landais, 63177, Aubière Cedex, France. C.Duroure@opgc.univ-bpclermont.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Duroure
authors.affiliation: Laboratoire de Parasitologie Générale, Département de Biologie Animale, Faculté des Sciences et Technologies, Université Cheikh Anta Diop, Dakar, Sénégal. toguebaye@ucad.sn.
authors.forename: Bhen S
authors.initials: BS
authors.lastname: Toguebaye
authors.affiliation: CIRAD, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, 34398, Montpellier, France. roger.frutos@cirad.fr.
authors.forename: Roger
authors.initials: R
authors.lastname: Frutos
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, B.P. 220, Dakar, Sénégal. niang@pasteur.sn.
authors.forename: Mbayame N
authors.initials: MN
authors.lastname: Niang
authors.affiliation: Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, UMR 6023, CNRS, 63177, Aubière, France. christian.vivares@orange.fr.
authors.forename: Christian P
authors.initials: CP
authors.lastname: Vivarès
authors.affiliation: Section of Infectious Disease and Department of Microbial Pathogenesis, Winchester Building WWW403D, Yale School of Medicine, 15 York St., New Haven, CT, 06520, USA. choukri.benmamoun@yale.edu.
authors.forename: Choukri
authors.initials: C
authors.lastname: Ben Mamoun
authors.affiliation: Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U1194 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d'Aurelle, 34298, Montpellier cedex 5, France. emmanuel.cornillot@univ-montp1.fr.|Institut de Biologie Computationnelle, IBC, Campus Saint Priest, 34090, Montpellier, France. emmanuel.cornillot@univ-montp1.fr.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Cornillot
mesh_terms: D001482:Base Composition; D016054:DNA, Protozoan / Q000235:genetics; D009670:Encephalitozoon cuniculi / Q000235:genetics*; D016678:Genome; D006790:Host-Parasite Interactions / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D016615:Telomere / Q000235:genetics*
chemical_list: D016054:DNA, Protozoan