Extended Data Fig. 9: Functional analysis of the fungal effector genes SIX1a and SIX4, which are present in the accessory region of chromosome 3 and were significantly induced upon host infection.

The ΔSIX1a and ΔSIX4 mutants were generated in the Foc TR4 II5 WT background using the standard one-step gene replacement strategy⁶⁹. The complemented strains ΔSIX1a-C (complemented FocΔSIX1a strain) and ΔSIX4-C (complemented FocΔSIX4 strain) were generated using whole effector genes and their native promoters combined with the neomycin resistance gene. Cavendish banana plantlets with four or five leaves were inoculated with mock (H₂O) or treated soil samples harboring conidia from different stains (5,000 conidia/g soil). The disease index (DI) distribution (top panel; see Methods) was calculated among 20 inoculated plants based on the DI from 0–−4: 0, no symptoms; 1, some brown spots in the inner rhizome; 2, <25% of the inner rhizome showing browning; 3, up to 75% of the inner rhizome showing browning; and 4, 100% of the inner rhizome and pseudostem dark brown (considered dead). The cross sections were sampled from inoculated plantlets (bottom panel) at 30 days post inoculation. The extent of discoloration is correlated with the DI distribution shown in the top panel.