Comments on revised manuscript

Thank you for the improvement of the manuscript. It is now easier to follow and includes more information as before. It was a bit difficult to see the changes as they were not highlighted and the lines are not numbered. Despite that, I have only a few minor comments that should be addressed easily so that the manuscript will be ready for publication soon. Line numbers in the comments refer to lines of the specific paragraph/section. DNA and RNA extraction: L7:such as? If you listed all tissues, please remove such as, if you sequenced RNA for nor tissues please add them. Sequencing and Assembly: L5: 159 bp is an uncommon read length. Was this just a typo, or how did that come to be? L10: remove "the" before juicer; otherwise, it sounds like an actual fruit juicer instead of a bioinformatics tool ;-). Same for 3D-DNA in the line below. Please make it more clear in the text if you sequenced the RNA for each tissue separately or in one library. L11-12: I am not convinced that not allowing for correction was the right approach. Did you test how the results would look with corrections enabled? Assembly Statistics and Quast Results: Quast calculates assembly statistics so I am not sure why the header needs to include both. L5: Please avoid using "better" but instead rephrase so that is is clear that the NG50 is 1.75x larger than the previous assembly. "Better" is not clear. Busco and Merqury results: I would not claim that Busco says the genome is 95% complete, as busco only tries to find genes that are supposedly orthologous in Actinopterygii. So I would rather say Busco suggests a high completeness as it finds 95% of the orthologs. Also, all genes in the Busco dataset are supposed to be single-copy orthologs; therefore, I would not say that 93% are conserved single-copy orthologs, as the remaining duplicated or fragmented genes could just be assembly errors. Please also state the Merqury QV value, and I would suggest stating the error rate in %. I still find the discussion about missing Busco genes strange, as since Busco 4 or 5 the datasets all got much larger and the Busco completeness values went down in most assemblies, even in well studies taxa as mammals. With recent datasets, it is very unlikely to get much more than 95-97%. In my opinion, it is rather a sign of too large and incorrect Busco datasets than evidence for missing orthologs. I would at least add that point to the discussion. Table 1: Please follow standard practice in scientific writing and add separators to the numbers in all tables (main text and supplementary), e.g., 28444102 → 28,444,102. Otherwise, they are difficult to read. Annotation Results: L3: 20,101 coding genes, 18,616 genes … Please check throughout the whole manuscript for consistent style. Data Availability: L2: Annotation report release 100. What does "100" stand for? Also, "at here" sounds not correct; please remove "at". L4: Table S2 does not show the scaffold identifiers. L5: please state the complete BioProject accession not just the numerical part. Supplementary data: Please change numbers in all tables to standard format e.g., 21,671,036