Telomere-to-Telomere assembly and annotation of Pinot Noir 40024

PN40024, a highly homozygous Pinot Noir inbred line, was used for T2T genome assembly. In total, we generated 39.12Gb (~65X coverage) HiFi reads by the PacBio platform. The preliminary assembly were conducted using Hifiasm on HiFi reads, and Mumer was used to order and orient the contig-level assemblies using the PN40024.v3 genome as the reference, forming 169 contigs representing 19 chromosomes.

     The PN40024.T2T genome size (494.87M) is longer than that of PN40024.v3 (426.18M). Due to the accuracy of HiFi long reads, the N50 length PN40024.T2T of (26.89 Mb) is 260 times higher than PN40024.v3 (~102Kb). For all 9423 gaps in PN40024.v3 assembly, PN40024.T2T assembly is the gap-free grape genome.To validate the quality of our assembly, K-mer and BUSCO were conducted. We used K-mer to evaluate genomic heterozygosity, estimated 99.8%. BUSCO to evaluate genomic completeness, about 98.5% of the core conserved plant genes were found complete in the genome assembly.

The PN40024.T2T genome assembly: PN40024.T2T.fa

The PN40024.T2T gene annotation: PN40024.gff

The PN40024.T2T TE annotation: PN40024.TE.gff

The PN40024.T2T centromere annotation: PN40024.trf.gff3

Comparison of gene annotation between PN40024.T2T, PN40024.v3,PN40024.v4 and PN40024.v4.1:gene_correlation.tsv