Assembly and annotation of Pinot Noir

Pinot Noir is one of the world's most famous grapes, with its late ripening light ruby red fruit., was used for T2T genome assembly. A total of 33,349,412,693bp HiFi reads with ~ 65x coverage were generated by the PacBio platform. The preliminary assembly were conducted using Hifiasm on HiFi reads. A total of 83,958,664,800 bp of Hi-C reads with ~ 160× coverage were used to anchor and remove some short contigs using Juicer. 3D-DNA was then used to obtain the genome at the scaffold level. The two T2T gap-free haplotypes of the hybrid Pinot Noir, PN1 (473.43MB) and PN2 (467.09MB).
To validate the quality of our assembly, K-mer and BUSCO were conducted. We used K-mer to evaluate genomic heterozygosity, estimated 1.43%. BUSCO to evaluate genomic completeness, about 98.3% in PN1 and 98.4%in PN2 of the core conserved plant genes were found complete in the genome assembly. For genome annotation, the number of genes identified by the genome is similar, more than 37,000 genes were found for Pinot Noir, PN1 (37037) PN2 (37350).

The PN1 genome assembly: PNhap1.fa

The PN1gene annotation: PNhap1.gff3

The PN1 TE annotation: PNhap1.TE.gff

The PN2 genome assembly: PNhap2.fa

The PN2gene annotation: PNhap2.gff3

 The PN2 TE annotation: PNhap2.TE.gff