Reviewer name and names of any other individual's who aided in reviewer	Kekun Zhang
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?	No
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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
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Is the data acquisition clear, complete and methodologically sound?	Yes
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Is there sufficient detail in the methods and data-processing steps to allow reproduction?	Yes
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Is there sufficient data validation and statistical analyses of data quality?	No
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Is the validation suitable for this type of data?	Yes
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Is there sufficient information for others to reuse this dataset or integrate it with other data?	No
Additional Comments
Any Additional Overall Comments to the Author	My main concerns: 1. Please explain why different sequencing methods were chosen for the genome assembly of Dakapo and Rubired, given that HiFi sequencing is currently mainstream and provides more accurate assembly? 2. Recently, the T2T level genome of many grape cultivars has been assembled including the reference genome PN_T2T and the teinturier grape Yan73, Please align with the latest complete reference genome PN_T2T in Line 172, and add the genome information about PN_T2T and Yan73 in Table 1. ( DOI10.1093/hr/uhad061, DOI10.1093/hr/uhad205 ) 3. Line 387-389: How did you verify the correctness of this inversion? Is it contained within a single contig without orientation or assembly errors in the Dakapo genome? Have you identified any other genomes with this inversion? 4. Line 255: can you explain why is the contig N50 so low? 5. Line 328: whether the total number of annotated genes in the two Rubired haplotypes are all 56,681? it would be more appropriate to describe them separately. 6. The phenotypes of these two grapes should be included, not just in the pattern diagram. 7. The sequence difference in Figure 2 should be verified using other methods, such as PCR results and Sanger sequencing.
Recommendation	Major Revision