An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue G3 Année : 2023

An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype

Amandine Velt
Bianca Frommer
  • Fonction : Auteur
Sophie Blanc
Daniela Holtgräwe
  • Fonction : Auteur
Eric Duchêne
Vincent Dumas
Jérôme Grimplet
  • Fonction : Auteur
Philippe Hugueney
Catherine Kim
  • Fonction : Auteur
Marie Lahaye
  • Fonction : Auteur
José Tomás Matus
  • Fonction : Auteur
David Navarro-Payá
  • Fonction : Auteur
Luis Orduña
  • Fonction : Auteur
Marcela K Tello-Ruiz
  • Fonction : Auteur
Nicola Vitulo
  • Fonction : Auteur
Doreen Ware
  • Fonction : Auteur

Résumé

The genome sequence of the diploid and highly homozygous Vitis 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 9 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 toward the eventual elaboration of the grapevine pangenome.
Fichier principal
Vignette du fichier
islandora_162691.pdf (1.07 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte

Dates et versions

hal-04094305 , version 1 (10-05-2023)

Licence

Paternité

Identifiants

Citer

Amandine Velt, Bianca Frommer, Sophie Blanc, Daniela Holtgräwe, Eric Duchêne, et al.. An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype. G3, 2023, 13 (5), ⟨10.1093/g3journal/jkad067⟩. ⟨hal-04094305⟩
49 Consultations
17 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More