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 PN_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 PN_T2T of (26.89 Mb) is 260 times higher than PN_v3 (~102Kb). For all 9423 gaps in PN_v3 assembly, PN_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.gff3

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

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

Comparison of gene annotation among PN_T2T and 12X.v0, 12X.v2, PN40024.v4, PN40024.v4.1: Gene connected list .xlsx