Reviewer name and names of any other individual's who aided in reviewer	Haimeng Li
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?	No
Additional Comments	The genomic annotation file is not publicly available.
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>	No
Additional Comments	Genomic annotation information and protein sequence information were not found in the NCBI database.
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?	No
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?	No
Additional Comments
Any Additional Overall Comments to the Author	The manuscript, 'Draft Genome of the Endangered Visayan Spotted Deer (Rusa alfredi), a Philippine Endemic Species,' contributes to the field of conservation genomics. The study presents the first draft genome assembly of the Visayan Spotted Deer, utilizing Illumina short-read sequencing technology to generate valuable genomic resources for this endangered species. Here are some questions and comments. Q1. Why was gene annotation conducted using only homology-based annotation? It is recommended that the annotation approach includes de novo, RNA-based, and homology-based methods. Combining these approaches would provide a more comprehensive gene set, particularly for species with limited genomic resources. Please revise the method section to include these additional annotation strategies. The authors have stated that due to sampling limitations, RNA-based experiments could not be conducted. RNA extraction might be performed using the tissue samples that were previously collected for genome assembly. In Lines 167-172 Q2. Before proceeding with genome assembly, it is essential to conduct a genome survey. This initial step provides crucial information about the genome's size, complexity, and composition, which is vital for planning the assembly strategy and selecting appropriate sequencing technologies and bioinformatics tools. The survey should include estimates of genome size, GC content, repetitive elements, and ploidy level. Additionally, the result could be used to assess the completeness of the assembly. Please include a section on the genome survey in the Method section. Q3. To enhance the quality and contiguity of the assembly, utilizing another species as a reference genome for scaffolding might introduce errors due to discrepancies in karyotype. It is essential to ascertain whether there is a definitive karyotype study that verifies the consistency of the karyotype between the Visayan Spotted Deer and the reference species, indicating the absence of chromosomal fission or fusion events. In Lines 236-238 This information is crucial for the reliability of the scaffolding process. Q4. Although the length of scaffold N50 is long, the high number of scaffolds and contigs suggests fragmentation. Have you addressed redundancy in the assembly? In Line 238 Q5. Have you used software like Merqury to detect assembly errors and assess the completeness of the assembly? This is useful for evaluating the quality of the genome sequence and identifying potential issues that may need to be addressed. Q6. Are the species divergent, which might explain the low number of orthologous genes? Is this an annotation issue or does it reflect true biological divergence? Further investigation into the annotation process and comparative genomic analyses may be warranted to understand the extent of divergence and the implications for the study. In Lines 313-317 Q7. Please standardize the format of numbers throughout the manuscript to maintain consistency in the number of significant figures. In Lines 224, 225, 227, 239, 245
Recommendation	Major Revision