e collected the young fresh leaf tissue at XX stage for total six samples from the vineyards operated by Cornell University, Geneva, New York (supplementary Table1).  High‐molecular‐weight genomic DNAs was isolated using KIT ( company name, website ) and purified using KIT (company name , website) following according to the manufacturer protocol.   The genomic DNA was quanlified with  Thermo Nanodrop™ XX Spectrophotometer (Thermo Fisher Scientific, https://www.thermofisher.com/) and further assessed by agarose gel electrophoresis.  [ template only The quantity of 100 gDNA was measured by Qubit® Fluorometric Quantitation (Life Technologies) and the 101 average length of the gDNA fragments was determined using the Agilent 2200 TapeStation 102 system using Genomic DNA ScreenTape (cat. 5067-5365) and Genomic DNA Reagents (cat. 103 5067-5366). The average fragment size of gDNA was > 60 Kb. The library was sequenced 120 on two lanes of an Illumina HiSeq 2500 sequencer in rapid run mode, using paired-end 121 sequencing to generate 580.55 M linked-reads with a mean read length of 139.5 bp after 122 trimming. The weighted mean molecule size was estimated as 63.18 Kb and mean read 123 coverage was ~ 68x. The WGS library preparation and sequencing was performed in the 124 Finnish Functional Genomics Centre (Turku, Finland). ]

de novo genome assembly

The linked-read data were assembled using Supernova v.2.0.1 assembler (Weisenfeld et 146 al. 2017)  with default settings. The assembler software was run for on a 28 core and 147 240 Gb RAM CSC – IT Center for Science cPouta virtual private server, based on Intel® 148 Xeon® CPU E5-2680 v.4 2.4 GHz processors The Busco score was calculated based on lineage-specific sets of Eudicotyledons odb10 with genome model (Busco: version 3.0.2, Augustus: Version 3.3 ).