Figure 3.

Splenic T_E repertoires elicited by Plasmodium chabaudi are highly diverse. (A) Simpson’s Diversity Index (SI) for UMI-size matched unchallenged T_N (green) and acute MT T_E repertoires (blue). SI varies from 0 to 1, and for T-cell receptor (TCR) repertoires represents the probability that identical TCRs (as determined by identical CDR3 amino acid sequence) will be drawn from the repertoire with two independent draws. SI of 0 therefore represents maximal diversity. (B) Each point in the strip plot represents a clone and the percentage of repertoire they occupy, for individual replicate mice for T_N unchallenged repertoires (green) and MT T_E repertoires (blue). Data for (A, B) was normalized by down-sampling to 5000 UMI. (C) Similarity between replicate repertoires is demonstrated using the Jaccard index, a normalized sharing metric which represents the degree of clonal overlap between repertoires. Jaccard index varies form 0 (no similarity) to 1 (identical repertoires). T_E replicate repertoires are more similar to each other in the acute phase of infection for both infection types. (D) Multi-dimensional-scaling (MDS) analysis using Jaccard similarity index of T_E repertoires for unchallenged (yellow), MT (blue) and SBP (red) repertoires. Data for (C, D) was normalized by down-sampling to 10⁴ reads and calculated on weighted data to include clonotype frequency.