Fig. 5: Expression of VSG phylotypes in the context of sequence similarity.

Combined transcript abundance for expressed phylotypes are plotted on to the phylotype sequence similarity network at a early (Peak 1), b middle (peaks 4–7), and c late (last peak) infection stages respectively. Data from four replicate animals are shown (A1–A4 from top to bottom). Nodes represent phylotypes and are labelled by phylotype number. Node size indicates the number of unique expressed transcripts, while node shade indicates the combined transcript abundance (log₂ CPM). The classical expectation of VSG expression is that a dominant VSG should subside in abundance and disappear as the host acquires antibody-mediated immunity. However, phylotypes were seen to persist across peaks and/or re-emerge later in the experiment; for instance, P40, P24 and P33 are present at all three time-points in A1, A2 and A3 respectively. Similarly, P2 was expressed strongly at the beginning and re-emerges at the end of infections in A1 and A2. Likewise, P44 was expressed at both the beginning and end of infection in A4. Since only three time-points are shown, it should be noted that these phylotypes were not present at all peaks, so this could represent re-emergence rather than persistence. In cases where sufficient nodes were expressed, the clustering coefficient (C) for their sub-network was calculated. This observed value was compared to mean average C for 100 randomised sub-networks of the same size. The ratio of the observed and expected (by chance) clustering coefficients for expressed sub-networks is shown where a calculation was possible. This value typically exceeds one showing that expressed nodes cluster more than random selections. When considered over all peaks, the clustering coefficient of expressed nodes is significantly higher than coefficients of randomised sub-networks of the same size (see Supplementary Fig. 10 for further details). Source data are provided as a Source Data file.