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.

Figure 1

(Opposite) Schematic representation of T.brucei chromosome II. Each predicted CDS >200 bp in length is represented by an arrow. The labels refer to the systematic name for each gene (see Table S1). The colours of the arrows represent the corresponding T.brucei GO assignment for each gene according to the Biological Process ontology (12). A set of high level GO categories were selected to represent the most informative high-level terms without overlapping paths in the GO hierarchy. Grey peaks reflect the GC skew scores calculated for a 2-kb window sliding in 1-kb increments. ‘Hypothetical proteins’ are proteins with no similarity to characterised proteins or with similarity to a hypothetical protein over less than 70% of the protein length. ‘Conserved hypothetical proteins’ are proteins with similarity to one or more hypothetical protein from an organism other than T.brucei over at least 70% of the protein length. ‘Trypanosoma brucei family hypothetical proteins’ are proteins with similarity with two or more T.brucei hypothetical proteins over at least 70% of the protein length. The predicted transmembrane domains are shown for proteins containing at least five domains. (Inset) Map of duplicated blocks on chrII. The copies of each putative duplicated block are classified by colour. Direction of arrowheads indicate the relative orientation of duplicated blocks. An enlarged version of this figure is included with the Supplementary Material (available at NAR Online).

Figure 2

(A) The physical map of chromosome II with the directional gene clusters and position of polymorphic mini- and microsatellite markers indicated. The physical distances between markers are shown (kb) and the genetic distances (cM) were calculated from recombination frequencies. Genetic distances shown are uncorrected. The relationship of physical and genetic maps to show hot and cold spots of recombination is also indicated (kb/cM). (B) Diagrams of the haplotypes of stock Tb927 showing 11 parental haplotypes shown as blue or yellow, and 27 recombinant types. White circles are unscored markers.