title: The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.
abstract: BACKGROUND
  Trypanosoma brucei gambiense is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a T. b. brucei isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between T. b. gambiense and the reference genome. We sought to identify features that were uniquely associated with T. b. gambiense and its ability to infect humans.
  
  
  RESULTS
  An improved high-quality draft genome sequence for the group 1 T. b. gambiense DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with T. b. brucei showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in T. b. gambiense DAL 972. A comparison of the variant surface glycoproteins (VSG) in T. b. brucei with all T. b. gambiense sequence reads showed that the essential structural repertoire of VSG domains is conserved across T. brucei.
  
  
  CONCLUSIONS
  This study provides the first estimate of intraspecific genomic variation within T. brucei, and so has important consequences for future population genomics studies. We have shown that the T. b. gambiense genome corresponds closely with the reference, which should therefore be an effective scaffold for any T. brucei genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in T. b. brucei, no T. b. gambiense-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Jackson
authors.forename: Mandy
authors.initials: M
authors.lastname: Sanders
authors.forename: Andrew
authors.initials: A
authors.lastname: Berry
authors.forename: Jacqueline
authors.initials: J
authors.lastname: McQuillan
authors.forename: Martin A
authors.initials: MA
authors.lastname: Aslett
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: Bridget
authors.initials: B
authors.lastname: Chukualim
authors.forename: Paul
authors.initials: P
authors.lastname: Capewell
authors.forename: Annette
authors.initials: A
authors.lastname: MacLeod
authors.forename: Sara E
authors.initials: SE
authors.lastname: Melville
authors.forename: Wendy
authors.initials: W
authors.lastname: Gibson
authors.forename: J David
authors.initials: JD
authors.lastname: Barry
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.forename: Christiane
authors.initials: C
authors.lastname: Hertz-Fowler
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D023061:Gene Order; D018503:Genome, Protozoan; D006801:Humans; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D026801:Synteny; D014347:Trypanosoma brucei gambiense / Q000235:genetics*; D014353:Trypanosomiasis, African / Q000469:parasitology*
chemical_list: D016054:DNA, Protozoan
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