The sequence and analysis of Trypanosoma brucei chromosome II

Nucleic Acids Res. 2003 Aug 15;31(16):4856-63. doi: 10.1093/nar/gkg673.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Antigens, Protozoan / genetics
  • Chromosome Mapping
  • Chromosomes / genetics*
  • DNA, Protozoan / chemistry
  • DNA, Protozoan / genetics*
  • Gene Duplication
  • Genes, Protozoan / genetics
  • Molecular Sequence Data
  • Pseudogenes / genetics
  • Recombination, Genetic
  • Sequence Analysis, DNA
  • Trypanosoma brucei brucei / genetics*

Substances

  • Antigens, Protozoan
  • DNA, Protozoan

Associated data

  • GENBANK/AC007862
  • GENBANK/AC007864
  • GENBANK/AC007865
  • GENBANK/AC007866
  • GENBANK/AC008031
  • GENBANK/AC008368
  • GENBANK/AC009463
  • GENBANK/AC012647
  • GENBANK/AC073246
  • GENBANK/AC079606
  • GENBANK/AE017150