SRX11317221 Illum_It2021 SRP322938 PRJNA735564 High molecular weight (HMW) DNA was extracted using a modified CTAB method on isolated nuclei. First, leaf tissues were ground in liquid nitrogen, and the powder was resuspended in the Beckman buffer (same as in our flow cytometric experiments). We then used 30m nylon circular filters (Partec, Germany) to remove tissue debris, and precipitated nuclei with 100g centrifugation under 4C for 20 minutes. HMW DNA was QCd on an agarose gel for length and quantified on a bioanalyzer. Unsheared HMW DNA was used to make Oxford Nanopore Technologies (ONT) ligation-based libraries (Oxford, UK). Libraries were prepared starting with 1.5ug of DNA and following all other steps in ONTs SQK-LSK109 protocol. Final libraries were loaded on an ONT flowcell (v9.4.1) and run on the GridION. Bases were called in real-time on the GridION using the flip-flop version of Guppy (v3.1). SRS9345982 I_taiwanensis2021 Illum_It2021 WGS GENOMIC size fractionation Illumina NovaSeq 6000 SRX11317222 ONT_It2021 SRP322938 PRJNA735564 High molecular weight (HMW) DNA was extracted using a modified CTAB method on isolated nuclei. First, leaf tissues were ground in liquid nitrogen, and the powder was resuspended in the Beckman buffer (same as in our flow cytometric experiments). We then used 30m nylon circular filters (Partec, Germany) to remove tissue debris, and precipitated nuclei with 100g centrifugation under 4C for 20 minutes. HMW DNA was QCd on an agarose gel for length and quantified on a bioanalyzer. HMW genomic DNA was used to construct Illumina (Illumina, USA) libraries for estimating genome size (above) and correcting residual errors in the ONT assembly. Libraries were constructed using the KAPA HyperPrep Kit (Kapa Biosystems, Switzerland) followed by sequencing on an Illumina NovaSeq6000 with 2x150 bp paired-ends. SRS9345982 I_taiwanensis2021 ONT_It2021 WGS GENOMIC size fractionation GridION