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Title: An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype
Authors: Velt, Amandine
Frommer, Bianca
Blanc, Sophie
Holtgräwe, Daniela
Duchêne, Éric
Dumas, Vincent
Grimplet, Jérôme
Hugueney, Philippe
Kim, Catherine
Lahaye, Marie
Tomás Matus, José
Navarro-Payá, David
Orduña, Luis
Tello-Ruiz, Marcela K
Vitulo, Nicola
Ware, Doreen
Rustenholz, Camille
Issue Date: 2023
Citation: G3-Genes Genomes Genetics, 2023
Abstract: 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.
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ISSN: 21601836
Appears in Collections:[DOCIART] Artículos científicos, técnicos y divulgativos

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