Cassava (Manihot esculenta Crantz), though a major world crop with enormous 
potential, is very under studied. Little is known about its genome structure and 
organisation. Transposable elements have a key role in the evolution of genome 
structure, and can be used as important tools in applied genetics. This paper 
sets out to survey the diversity of members of three major classes of 
transposable element within the cassava genome and in relation to similar 
elements in other plants. Members of two classes of LTR-retrotransposons, 
Ty1/copia-like and Ty3/gypsy-like, and of Enhancer/Suppressor Mutator 
(En/Spm)-like transposons were isolated and characterised. Analyses revealed 59 
families of Ty1/copia, 26 families of Ty3/gypsy retrotransposons, and 40 
families of En/Spm in the cassava genome. In the comparative analyses, the 
predicted amino acid sequences for these transposon classes were compared with 
those of related elements from other plant species. These revealed that there 
were multiple lineages of Ty1/copia-like retrotransposons in the genome of 
cassava and suggested that vertical and horizontal transmission as the source of 
cassava Mecops may not be mutually exclusive. For the Ty3/gypsy elements 
network, two groups of cassava Megyps were evident including the Arabidopsis 
Athila lineage. However, cassava En/Spm-like elements (Meens) constituted a 
single group within a network of plant En/Spm-like elements. Hybridisation 
analysis supported the presence of transposons in the genome of cassava in 
medium (Ty3/gypsy and En/Spm) to high (Ty1/copia) copy numbers. Thus the cassava 
genome was shown to contain diverse members of three major classes of 
transposable element; however, the different classes exhibited contrasting 
evolutionary histories.