ZUP1 and infection: Sequence comparisons between first and second infections revealed four categories of the genes that have accumulated the majority of the SNPs including (i) genes associated with Ct virulence such as CTA_0498/tarP, CTA_0166 (phospholipase D-like protein PDL), and CTA_0948 (DUB); (ii) CTA_0021/ileS associated with amino acid metabolic process; (iii) CTA_0484/omcA associated with Ct extracellular matrix; and (iv) CTA_0140 that is involved in transport and trafficking pathways (Fig. 8 and Table S6) [66,73, 75, 89, 91].