PN40024_T2T_Genome

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome consisted of thousands of fragments with missing centromeres and telomeres, which limited the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) was 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome, therefore, constitutes an important resource for grapevine genetic studies and breeding programs.

Keywords: Viticulture, T2T, gap-free, gene cluster, centromere, telomere, inbreeding

Methods for assembling high-quality genomes

Genome-Wide-Annotation-Pipeline

To find telomeres and centromeres

Pan-genome TE Annotation Pipeline

Assembles High-diversity Regions

Data availability

All PacBio sequence data have been deposited in the NCBI Sequence Read Archive under project number PRJNA882193 and the National Genomics Data Center (NGDC) Genome Sequence Archive (GSA) (https://ngdc.cncb.ac.cn/gsa/), with BioProject number PRJCA012093. The assembly and annotation as well as the sequences of centromeres and heterozygous regions have been deposited in zenodo: https://zenodo.org/record/7751391#.ZBgVmcJBy3A. The assembly and its annotation will be also hosted in the GRAPEDIA portal (https://grapedia.org/).

Citations

Shi, Xiaoya, et al. "The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding." Horticulture Research (2023): uhad061.

If you have any questions, please feel free to contact: Yongfeng Zhou: zhouyongfeng@caas.cn