Reviewer name and names of any other individual's who aided in reviewer	Camille Rustenholz
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	Yes
Please add additional comments on language quality to clarify if needed
Are all data available and do they match the descriptions in the paper?	Yes
Additional Comments
Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a>	Yes
Additional Comments
Is the data acquisition clear, complete and methodologically sound?	Yes
Additional Comments
Is there sufficient detail in the methods and data-processing steps to allow reproduction?	No
Additional Comments	Overall, the authors give enough details except for the haplotypes of Chardonnay, Pinot noir, Cabernet sauvignon and Cabernet franc that were used for Figure 3.
Is there sufficient data validation and statistical analyses of data quality?	Yes
Additional Comments
Is the validation suitable for this type of data?	No
Additional Comments	Overall, the authors provide accurate validation for this type of data except for the inversion that was identified on chromosome 10 of Dakapo assembly. In my opinion, more evidences need to be provided as Dakapo contigs were anchored using PN40024 12X.v2 assembly version. There is indeed a heterozygous region at the beginning of chromosome 10 in PN40024 genome which makes its assembly and scaffolding quality quite doubtful at that exact location and especially for this assembly version. I would suggest to check it using the latest PN40024 T2T version (Shi et al., Hort Res 2023) and to show some Dakapo short read alignments against its own assembly to validate the borders of this inversion, even though some wet lab validation would be even more convincing.
Is there sufficient information for others to reuse this dataset or integrate it with other data?	Yes
Additional Comments
Any Additional Overall Comments to the Author	The authors provided the assemblies and gene annotations of the genomes of two teinturier varieties, Dakapo and Rubired. Dakapo was assembled using a combination of Nanopore and Illumina reads whereas Rubired was assembled using PacBio HiFi reads. Even though both assemblies are of high quality, quality metrics are better for Rubired assembly than for Dakapo assembly, in terms of contiguity and of phasing. I would have liked the authors to comment and explain these differences more extensively maybe in a dedicated paragraph in the Discussion section: - Why Dakapo assembly could not be phased? - Are these differences in terms of quality due to the sequencing technologies (Nanopore versus PacBio HiFi) used? Or to different year of dataset acquisition? Or to assembly methods? Both assemblies were also annotated: 36,940 genes in the Dakapo assembly and 56,681 genes in the diploid Rubired. I assume that 56,681 is the sum of the number of genes annotated on haplotype 1 and haplotype 2 of Rubired. If so, it needs to be clearly stated line 328 otherwise it can be confusing for the reader who will think that Rubired has 20,000 more genes than Dakapo. Also, the authors used two different annotation pipelines, which complicates the gene content comparison and the synteny analysis later on. I would have liked the authors to comment and explain it: - Is it due to the difference in the quality of the assemblies? If so, the authors need to highlight the limits of their annotation pipeline regarding assembly quality. - Any other explanation? Some minor suggestions : - Line 74: please use the word “clone” in the sentence for a matter of clarity. - Line 292-293: PN40024.v4 assembly is not the most recent but the PN40024 T2T is (Shi et al., Hort Res, 2023) The quality of the assemblies and annotations are very good and the resources of the paper will be very valuable for the grapevine community, especially to study the anthocyanin production in grapevine.
Recommendation	Minor Revision