Reviewer name and names of any other individual's who aided in reviewer	Mile Sikic
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?	Yes
Additional Comments
Is there sufficient data validation and statistical analyses of data quality?	Yes
Additional Comments
Is the validation suitable for this type of data?	Yes
Additional Comments
Is there sufficient information for others to reuse this dataset or integrate it with other data?	Yes
Additional Comments	In their update to the previous study on the comparison of long read technologies for sequencing and assembly of plant genomes, Sharma et al. presented a follow-up analysis using a newer generation of basecallers for nanopore reads and PacBio HiFi reads. I argue that this study is an important update, but it is not suitable for publication in the current form. My major comments are the following: 1. It is not clear which version of the basecaller the authors used in assemblies related to Table 1 and Table 3 2. For phased assemblies, it is important to provide information about the size of alternative contigs 3. In Table 1, it would be great to have results for methods that do not phase assembly (i.e. Flye) 4. There is no explanation why authors use IPA instead of other HiFi assemblers, i.e. hifiasm, which from my experience, perform better than IPA 5. A sentence related to Table 3, “The quality of the assemblies was more contiguous with less data in each of these cases when HiFi reads were used instead of the earlier continuous long reads (Table 3).” is not clear. Following Table 3, assemblies achieved using long reads have similar or longer N50 and higher BUSCO score. Also, it is not clear which assembler was used for long reads
Any Additional Overall Comments to the Author
Recommendation	Major Revision