Comments on revised manuscript

Different cs line could have variation in inversions, insertions, translocations, tandem repeats, using a different accession to anchor and order of contigs could introduced bias or even errors. Using linkage map or Hi-C data from the same accession to do scaffolding is better but needs a lot of lab and bioinformatics work, which may not be realistic. The final genome assembly is significantly larger than the estimated genome size from a different cs line, I still suggest the authors do a k-mer analysis to validate the genome size further using Illumina or PacBio reads. The author of RaGOO said “RaGOO does not account for potential haplotype duplication in any way. Likely, such overlapping contigs will end up getting placed right next to each other in the final pseudomolecules. If one believes these duplications may exist in their assembly, I encourage them to use tools like purge_haplotigs prior to using RaGOO (https://github.com/malonge/RaGOO/issues/23).” Hence, the author needs to remove the potential redundancy in the final assembly.