Multiple causes of size variation in the diploid megabase chromosomes of African tyrpanosomes

The chromosomes of many protozoans are polymorphic in size, but African trypanosomes contain diploid homologues which are exceptionally size-polymorphic. We present the first complete analysis of the structure of a Trypanosoma brucei megabase chromosome which reveals the concentration of repetitive sequence, non-random distribution of transposon-like elements, and a hemizygous variant surface glycoprotein gene expression site. Subsequent comparative analyses of size-polymorphic homologues show that the repetitive regions are highly polymorphic, as demonstrated in studies on the chromosomes of other protozoan parasites. We show that a large number of the transposon-like elements are located in these regions. However, although we have shown elsewhere that synteny is maintained in coding regions, homologous chromosomes may vary along their entire length. Thus, the variable chromosomal location of variant surface glycoprotein expression gene sites, the expansion and contraction of repetitive DNA, the number of putative transposons, sequence polymorphism at chromosome ends, and expansion and contraction within or between coding regions all contribute to huge chromosomal size polymorphisms in T brucei.