title: The sequence and analysis of Trypanosoma brucei chromosome II.
abstract: We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.
authors.affiliation: The Institute for Genomic Research, Rockville, MD 20850, USA. nelsayed@tigr.org
authors.forename: Najib M A
authors.initials: NM
authors.lastname: El-Sayed
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.forename: Jinming
authors.initials: J
authors.lastname: Song
authors.forename: Annette
authors.initials: A
authors.lastname: MacLeod
authors.forename: Frederic
authors.initials: F
authors.lastname: Bringaud
authors.forename: Christopher
authors.initials: C
authors.lastname: Larkin
authors.forename: David
authors.initials: D
authors.lastname: Wanless
authors.forename: Jeremy
authors.initials: J
authors.lastname: Peterson
authors.forename: Lihua
authors.initials: L
authors.lastname: Hou
authors.forename: Sonya
authors.initials: S
authors.lastname: Taylor
authors.forename: Alison
authors.initials: A
authors.lastname: Tweedie
authors.forename: Nicolas
authors.initials: N
authors.lastname: Biteau
authors.forename: Hanif G
authors.initials: HG
authors.lastname: Khalak
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Lin
authors.forename: Tanya
authors.initials: T
authors.lastname: Mason
authors.forename: Linda
authors.initials: L
authors.lastname: Hannick
authors.forename: Elisabet
authors.initials: E
authors.lastname: Caler
authors.forename: Gaëlle
authors.initials: G
authors.lastname: Blandin
authors.forename: Daniella
authors.initials: D
authors.lastname: Bartholomeu
authors.forename: Anjana J
authors.initials: AJ
authors.lastname: Simpson
authors.forename: Samir
authors.initials: S
authors.lastname: Kaul
authors.forename: Hong
authors.initials: H
authors.lastname: Zhao
authors.forename: Grace
authors.initials: G
authors.lastname: Pai
authors.forename: Susan
authors.initials: S
authors.lastname: Van Aken
authors.forename: Teresa
authors.initials: T
authors.lastname: Utterback
authors.forename: Brian
authors.initials: B
authors.lastname: Haas
authors.forename: Hean L
authors.initials: HL
authors.lastname: Koo
authors.forename: Lowell
authors.initials: L
authors.lastname: Umayam
authors.forename: Bernard
authors.initials: B
authors.lastname: Suh
authors.forename: Caroline
authors.initials: C
authors.lastname: Gerrard
authors.forename: Vanessa
authors.initials: V
authors.lastname: Leech
authors.forename: Rong
authors.initials: R
authors.lastname: Qi
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: David
authors.initials: D
authors.lastname: Schwartz
authors.forename: Tamara
authors.initials: T
authors.lastname: Feldblyum
authors.forename: Steven
authors.initials: S
authors.lastname: Salzberg
authors.forename: Andrew
authors.initials: A
authors.lastname: Tait
authors.forename: C Michael R
authors.initials: CM
authors.lastname: Turner
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Ullu
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: Sara
authors.initials: S
authors.lastname: Melville
authors.forename: Mark D
authors.initials: MD
authors.lastname: Adams
authors.forename: Claire M
authors.initials: CM
authors.lastname: Fraser
authors.forename: John E
authors.initials: JE
authors.lastname: Donelson
mesh_terms: D000818:Animals; D000953:Antigens, Protozoan / Q000235:genetics; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics*; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics*; D020440:Gene Duplication; D017125:Genes, Protozoan / Q000235:genetics; D008969:Molecular Sequence Data; D011544:Pseudogenes / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D000953:Antigens, Protozoan; D016054:DNA, Protozoan