Twenty-two genes from the “pks15” cluster 30, NRP clusters 7, 31, 35, 41, and 42, T1-PKS clusters 25, hybrid NRP-T1PKS clusters 19 and 29, fungal-RiPP clusters 3, 4, 8, 11, 15, and 16, hybrid NRP, fungal-RiPP cluster 26, and terpene cluster 6 were upregulated in the WT in vivo (vs. WT in vitro) 2–9 fold throughout the infection period, but noticeably downregulated in Δpks15 in vivo (vs. WT in vivo) 1–5 fold at 48 h and 72 h (Figure 6 and Supplementary Table S5). Here, ARAF is linked to infection.