Genomic tips 100 g kit

Total DNA was extracted using the MagAttract HMW DNA Kit (Qiagen) according to manufacturer’s instructions and used for short-read sequencing. Sequencing libraries were prepared using a Nextera XT library prep kit (Illumina GmbH, Munich, Germany) for a 250 bp paired-end sequencing run on an Illumina MiSeq platform. The obtained reads were de novo assembled with the Velvet assembler integrated in the Ridom SeqSphere+ v. 7.0.4 software (Ridom GmbH, Münster, Germany).
DNA extraction for long-read sequencing was performed using the Genomic-Tips 100/G kit and Genomic DNA Buffers kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the 1D Ligation Sequencing Kit (SQK-LSK109) in combination with Native Barcoding Kit (EXP-NBD104; Oxford Nanopore Technologies, Oxford, United Kingdom) and were loaded onto a R9.4 flow cell (Oxford Nanopore Technologies). The run was performed on a MinION MK1b device. Collection of raw electronic signal data and live base-calling was performed using the MinKNOW software and the Guppy basecaller (Oxford Nanopore Technologies). The long-reads were assembled using ONT assembly and Illumina polishing pipeline (Oxford Nanopore Technologies), performing Canu assembly followed by polishing steps, including pilon and BWA mem mapping using the Illumina reads.³

Genomic DNA of isolates 67659 and 72554 was extracted using the Genomic-Tips 100/G kit and genomic DNA buffers kit (Qiagen, Hilden, Germany). Libraries were prepared using the ligation sequencing kit (SQK-LSK109), combined with a native barcoding kit (EXP-NBD104) and the rapid barcoding kit (SQK-RBK004) (Oxford Nanopore Technologies, Oxford, United Kingdom), and were loaded onto an R9.4 flow cell (Oxford Nanopore Technologies). Genomes were assembled with a hybrid approach using Unicycler version 0.4.4 (19 (link)) with default parameters.

DNA extractions of young leaves of cv. “Pinot noir” clone 162 (ID code FRA038-193.Col.162), cv. “Schiava grossa” (synonymous “Trollinger”, ID code FRA038-2525.Col.1), and cv. “Helfensteiner” (ID code FRA038-2744.Col.1) were performed as described by Merdinoglu et al. (2005) (link). Illumina DNA PCR-Free Prep kit was used to prepare the resequencing libraries according to provider procedures. Paired-end Illumina HiSeq 4000 sequencing at about 15× coverage was performed for “Pinot noir” and “Schiava grossa”, respectively. Paired-end Illumina NovaSeq 6000 sequencing at about 15× coverage was performed for “Helfensteiner”.
One gram of young leaves (1 cm²) of PN40024 (ID code FRA038-40024.Col.1) was collected and DNA was extracted using QIAGEN Genomic-tips 100/G kit. SMRT sequencing on a Sequel I machine (3 SMRTCells; PacBio) and dedicated library preparation were performed according to provider procedures.
Genotyping-by-sequencing (GBS) was performed on the population “Riesling” × “Gewurztraminer” [exhaustively described by Duchêne et al. (2020) (link) using the procedure described by Girollet et al. (2019) (link)].
All data generated in the frame of this study were submitted under the ENA Study Accession PRJEB45423.