Segmental gene conversion occurs readily during infection.

<p>(A) The top diagram represents a multiple sequence alignment between clone 03-32c07 and its three putative donors 14-A (A), 14-B (B) and 14-C (C). The diagram runs 5′ to 3′ left to right. Mismatches between the clone sequence and each individual donor are indicated by black bars. The most parsimonious pattern, minimising the number of contributing segments and mismatches, is highlighted, and is summarized in the lower diagram. Segment contribution was inferred when there was >1 nt difference from the donor contributing surrounding segments. In the lower diagram, dotted and bold lines divide the sequence into the regions encoding the N-terminal signal peptide, the mature NTD, the mature CTD, and the GPI-anchor signal sequence. Black bars projecting from the top of the diagram indicate conserved cysteine codons, and black bars spanning and projecting from the bottom of each diagram indicate the positions of putative point mutations, where the expressed VSG differed from all identified donors. (B) Summaries of six example mosaic <i>VSG</i>s, from Set_14 (top), Set_10 (middle), and Set_04 (bottom). Diagrams were drawn as in (A). Different colours represent segments contributed by different donors; no donor sequence data was available for the regions coloured in white (3′ donations in Set_04). (C)Summaries of three 3′ donation events. Diagrams were drawn as in (A). Pairwise nucleotide identities between the expressed VSGs, 5′ and 3′ of the boundary of 3′ donation (indicated by the long dotted line), are given (%).