For de novo sequenced vines, rapidly expanding leaves about two centimeter (cm) long were collected for six samples from vineyards in Geneva, New York (supplementary Table1).  High‐molecular‐weight (HMW) genomic DNA (gDNA) was isolated using a CTAB protocol (Supplementary File) modified from Japelaghi et al. (2011) and Haley et al. (2014)\cite{Japelaghi_2011,Healey_2014}.  The genomic DNA was quantified with Quant-iT kits measured by Qubit-based fluorescence (Thermo Fisher Scientific), quality checked with Thermo Nanodrop™ 2000 Spectrophotometer (Thermo Fisher Scientific), and size estimated by Pulsed Field Gel Electrophoresis.  The bulk of the gDNA smear was required to be > 60 kb before further processing, and was typically centered on 100 kb. For seven of the genomes listed in Supplementary Table 1, HMW DNA was shipped to 10X Genomics (10X Genomics Inc., Pleasanton, CA, USA) for preparation and sequencing of libraries following their standard protocols (10X Genomics; Pleasanton, CA). Each 10X Genomics library was sequenced between 32- and 66-fold coverage using an Illumina NovaSeq sequencer to generate linked-reads with a mean read length of 139.5 bp after trimming. The weighted mean molecule size was estimated as 63.18 kb and mean read 123 coverage was ~ 68 fold. The whole genome sequencing (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\cite{Weisenfeld_2017} with default settings. 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).