Arabidopsis thaliana isolate:Arabidopsis wild-type Col-0 mutants Genome sequencing. Arabidopsis thaliana isolate:Arabidopsis wild-type Col-0 mutants

PacBio short (<50 bp) and low quality (QV < 80) reads were filtered out using the SMRTLink5 package. PacBio long reads were de novo assembled with the Flye tool (Kolmogorov et al., 2019) and polished with the Arrow tool from the SMRTLink5 package after remapping with the pbmm2 (minimap2) tool. The resulting assembly was further corrected to remove small-scale assembly errors with bcftool based on the mapping generated from Illumina short reads using BWA (Li & Durbin, 2009). Final chromosome-level assembly was done based on the synteny alignment with the Col-0 TAIR10 reference genome using MUMmer4 and the Perl scripts describe by (Jiao & Schneeberger, 2020). Gene annotation was done using the tool liftoff with the TAIR10 reference annotation. TEs were annotated with RepeatMasker (http://www.repeatmasker.org).