Reviewer name and names of any other individual's who aided in reviewer	Jin Sun
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Any Additional Overall Comments to the Author	Gomes-dos-Santos et al., have upgraded the freshwater mussel Margaritifera margaritifera genome with the usage of long-read sequencing. Overall, this version has been dramatically improved compared to the former one, with the increased N50 value and BUSCO score and decreased No. of contigs. Considering the important economic value of M. margaritifera and the high quality of assembly, I must congratulate the authors on this. However, in contrast to the high-quality assembly, I am a bit aware of the genome annotation part. To me, the number of gene models predicted is a bit higher compared with other molluscan genomes. This can also be reflected by the low proportion of gene models that can be annotated by Swissprot or GO etc. I suspect that the high number of gene models could be the consequence that only the ab initio evidence was applied in the current study. More sophisticated ways, such as EVM or maker, shall be used to see whether the number of gene models can be reduced without sacrificing the BUSCO scores on the gene models. Line 76, The official name shall be “Oxford Nanopore Technology (ONT)”. Fig. 1, it is interesting to see the wide distribution of M. margaritifera. I am a bit interested to know whether there are any genetic differentiations between the European population and the North American population.
Recommendation	Minor Revision