The genome sequence of the diploid and highly homozygous V. vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements to the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, being nearly homozygous, this genome contains several heterozygous regions that are yet to be resolved. Taking the opportunity of improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased with a total number decreasing from 2,059 to 640 and a reduction in N bases of 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the number of unplaced scaffolds was reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation of 35,230 genes to date. Finally, we demonstrated that PN40024 resulted from nine selfings of cv. ‘Helfensteiner’ (cross of cv. ‘Pinot noir’ and ‘Schiava grossa’) instead of a single ‘Pinot noir’. These advances will help maintain the PN40024 genome as a gold-standard reference, also contributing towards the eventual elaboration of the grapevine pangenome.

The genome sequence assembly of the diploid and highly homozygousV.viniferagenotype PN40024 serves as the reference for many grapevine studies. Despite several improvements of the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, despite the PN40024 genome is nearly homozygous, it still contains various heterozygous regions. Taking the opportunity of the improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences and considering that severalVitissp. genomes have recently been assembled with these approaches, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased. The number of scaffolds decreased from 2,059 to 640 and the number of N bases was reduced by 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the amount of unplaced scaffolds were reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow forVitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation to date of 35,230 genes. Finally, we demonstrate that PN40024 resulted from selfings of cv. ′Helfensteiner′ (cross of cv. ′Pinot noir′ and ′Schiava grossa′) instead of a single ′Pinot noir′. These advances will help maintaining the PN40024 genome as a gold-standard reference also contributing in the eventual elaboration of the grapevine pangenome.

The phylloxera resistant rootstock cultivar ′Boerner′ is an interspecies hybrid derived from Vitis riparia and V. cinerea and a valuable resource for Vitis disease resistances. We created a fully phased, high-quality ′Boerner′ genome sequence named BoeRC using long PacBio reads. Comprehensive gene annotation of both ′Boerner′ haplotypes, designated BoeRip and BoeCin, was applied to describe the phylloxera resistance locus Rdv1. Using a mapping population derived from a sensitive V. vinifera cultivar and ′Boerner′, the Rdv1 locus was further delimited. Rdv1, which is derived from V. cinerea and in-cluded in the haplotype BoeCin, was compared with sequences of phylloxera suscepti-ble and phylloxera tolerant cultivars. Between flanking regions that display high synteny, we detected and precisely characterized a diverse sequence region that covers between 202 to 403 kbp in different haplotypes. In BoeCin, five putative disease re-sistance genes were identified that represent likely candidates for conferring resistance to phylloxera.

Genomic long reads of the interspecific grapevine rootstock cultivar 'Börner' (Vitis riparia GM183 ϫ Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes, including the RNA editing sites. The organelle genomes in 'Börner' were maternally inherited from Vitis riparia. Citation Frommer B, Holtgräwe D, Hausmann L, Viehöver P, Huettel B, Töpfer R, Weisshaar B. 2020. Genome sequences of both organelles of the grapevine rootstock cultivar 'Börner.' Volume 9 Issue 15 e01471-19 mra.asm.org 1 on July 7, 2020 by guest http://mra.asm.org/ Downloaded from annotate plastid IR enabled, HMMER profile search [9] enabled, reference sequence V. vinifera chloroplast annotation [6], and MPI-MP chloroplast references enabled; specific settings for mt_Boe: reference sequence V. vinifera mitochondrion annotation [7]; settings for both: tRNA annotators tRNAscan-SE v2.0 [10, 11], ARAGORN v1.2.38 [12]with "Allow overlaps" and "Fix introns" enabled) (13), which uses OGDRAW v1.3 (14, 15) to visualize the annotation (Fig. 1). RNA editing sites were determined (16) using RNA-Seq data from five different 'Börner' tissues. A total of 133 genes with 90 editing

Genomic long reads of the interspecific grapevine rootstock cultivar 'Börner' (Vitis riparia GM183 x Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes including the RNA-editing sites. The organellar genomes were maternally inherited to 'Börner' from Vitis riparia.