design: Samples were pooled by amplicon taking 1.5 l from each barcoded product. Each amplicon pool was cleaned using AMPure XP beads using a bead ratio of 0.8x. Library preparation and sequencing was carried out at the Functional Genomics Centre Zurich (FGCZ). Two SMRTbell libraries were prepared for each amplicon length using the SMRTbell prep kit 3.0. One for the long 3-kb amplicons, one for the 1.5kb 16S and ITS amplicons. Size selection was performed using BluePippin (Sage Science) with a 0.75% dye-free cassette for each library. PacBio sequencing was performed on a Sequel II machine with the SMRT 8M cell. Two sequencing runs were performed, the first one using SMRT Link version 10.1 and the second one SMRT Link version 11.1. The first run encompassed all leaf samples, and the second one all mock samples.