The protocols and the work seem technically sound but would profit from more details. For example, it is mentioned that pools of specimens were used for sequencing but not why this was done.  ** We agree that our wording was confusing so we rewrote the text to clarify the issue “Extraction of high molecular weight DNA, construction of Pacific Biosciences HiFi circular consensus DNA sequencing libraries, and sequencing on Pacific Biosciences SEQUEL II (HiFi) instrument was performed by Delaware Biotechnology Institute, University of Delaware (DE, USA) using a pool of 20 specimens (Accession number: SAMEA113414145 qmTetScab1). Hi-C data was generated from another pool of 20 individuals from the same collection site (Accession number: SAMEA118091338) using the library preparation Omni-C DNA and sequenced 2 x 150 pb on the Illumina NovaSeq 6000 S4 instrument at the Centre Nacional de Seqüenciació Genòmica (CNAG), Barcelona, Spain."

Details on DNA extraction and library preparations are missing. To reproduce the work or to apply it to other systems, it is necessary to know what kits, reagents, and protocols were used. ** For the HIFI sequencing, a DNA library was prepared using the PacBio SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences of California, CA, USA) following the official protocol. Approximately 300 ng of high-quality genomic DNA was sheared to ~15–20 kb, repaired, and ligated with SMRTbell adapters to create circular molecules. The library was size-selected to remove fragments smaller than 1,000 bp, purified with AMPure PB beads, and quality-checked using Qubit and TapeStation. Finally, it was sequenced on the PacBio Sequel II platform in CCS mode to generate highly accurate HiFi reads suitable for genome assembly and analysis. These previous steps were performed in the University of Delaware (USA). **  Hi-C libraries were prepared using the Omni-C Dovetail protocol (Cantara Bio, CA, USA). Briefly, chromatin was extracted from frozen tissue and crosslinked with formaldehyde to preserve the native three-dimensional genome architecture by stabilizing DNA-protein and DNA-DNA interactions within the nucleus. The crosslinked chromatin was then fragmented using DNase I, and spatially proximal DNA ends were ligated to capture physical interactions between genomic regions, providing long-range linkage information useful for validating and scaffolding genome assemblies. Hi-C library preparation and sequencing were performed at the Centre Nacional d’Anàlisi Genòmica (CNAG), Barcelona, Spain.

To replicate the assembly process and subsequent assembly modification the parameters used for the software are missing. Especially, what parameters were used for hifiasm? Given it was not designed for assembly of multiple specimens’ genomes, were the parameters adjusted accordingly? It seems hifiasm had issues in the collapsing step since the authors applied purge_dups, which lead to a great reduction in the number of contigs. It is normally not desired to purge haplotigs from hifiasm assemblies and if applied does not result in such a drastic reduction in the number of contigs. I missed discussion of all of this.  ** The number of haplotypes was considered using the --nhap parameter in hifiasm. Given that our species is presumably diploid, as estimated by Smudgeplot, and the sequencing pool i ncluded 20 individuals, the parameter was set to nhap=40. However, d ue to the presence of multiple individuals, hifiasm may struggle to accurately resolve haplotypes, which may necessitate the use of purge_dups to remove redundant contigs.  ** We suspect that most of the duplications are due to the DNA being sourced from a pool of 20 individuals, as a single individual did not provide enough material to construct a HiFi library. We clarify this question in the main text “The genome size was estimated using GenomeScope2 (Vurture et al., 2017), and diploidy was confirmed with Smudgeplot (Ranallo-Benavidez et al., 2020). Assembly was conducted using hifiasm (Cheng et al., 2021) with n_hap=40 (considering diploidy and 20 individuals). Larger number of Haplotypic duplications presumably caused by the high number of specimens used for DNA extraction were withdrawn with purge_dups (Guan et al., 2020), passing from 2208 to 1272 contigs". We would like to point out that final genome size after purging duplicates and removing contamination matched the size initially predicted by Genomescope.

 “individuals that were not externally cleaned so it could also contain DNA from microbial and other eukaryote contaminants”. Why were the individuals not cleaned before assembly despite that this is known to cause assembly issues? ** Specimens were isolated from well water and individually collected to minimize contamination from other macroscopic species. However, this approach did not prevent contamination by microscopic organisms.

 It is not clear how many contigs remained after each step in the methods. What was the number of contigs after Hi-C scaffolding? In the method is says 821. It also says 59 contigs were obtained after applying BlobToolKit. Are the other 762 (821 - 59) contigs from contaminants? How does that align with the 322 contigs mentioned in Table 2 and the 17 scaffolds mentioned in the Results? ** We rewrote the text to be more sound and included a new sentence in the Methods section.

 "The coverage obtained has not been sufficient to deduce sex-linked chromosomes". Would this be a sensible analysis given the pools of specimens? Why is 53.8x coverage not enough? Is this the haploid sequence coverage? From Figure 4, the coverage seems twice as high. ** Several factors hindered the identification of sex chromosomes in our diploid species. Most prominently, the characteristic haploid coverage pattern typically associated with sex chromosomes was absent. Furthermore, the genome assembly and scaffolding were performed using two separate DNA pools without prior knowledge of the individuals’ sex, complicating the detection of sex-specific sequences. In addition, the lack of biological information on the species and genus—particularly whether sex determination is chromosomal or genetic—further limits the applicability of standard methods for identifying sex chromosomes.

The genome is available from NCBI. However, there are no annotations provided. At least a description of the repetitive content would be valuable. Repetitive content seems to have been assessed since assemblies were "preprocessed to mask repetitive and low-complexity regions". ** We added the annotation for the repetitive sequences as requested.

The completeness of the assembly was assessed using BUSCOs and k-mers. Given the chromosome-level assembly, it would be valuable to describe the sequence content and arrangement, and the structural variation. For example, what is the telomeric end repeat motif; what characterizes the centromeres (GC content, sequence content, repeat content); what is the distribution of repeat versus genic content? ** We present a new table summarizing the chromosomal location, composition, and sequences of the repetitive DNA elements.

 It would be important to know the average read lengths or read length N50s. ** The read length N50 of PacBio raw reads has been added to the results section.

The keywords should include the full species name. ** The species name has been added to the keywords section.

Are there assembly gaps? What is their size? ** The final assembly contains 299 gaps, each 100 bp in length. This is due to the default behavior of tools such as Hifiasm, YAHS, and PretextMap, which insert standardized 100 bp gaps when the true gap size cannot be determined.

There is no phylogenetic analysis. I suggest including one or refer to a previous solid (whole genome) phylogeny. ** We appreciate the suggestion to include a phylogenetic analysis. However, given the current lack of available genomic data from other species in the Pericarid crustacean order, we believe that conducting a robust phylogenetic analysis at this stage would not be sufficiently reliable. We agree that such an analysis would be highly valuable, particularly once more genomic data from related taxa becomes available, and it is a future goal of our research group.