The sequence and analysis of Trypanosoma brucei chromosome II

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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.