Reviewer name and names of any other individual's who aided in reviewer	Masaomi Hatakeyama
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?	Yes
Additional Comments
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>	Yes
Additional Comments
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?	Yes
Additional Comments	The authors wrote, in line 306, Supplementary information regarding the computational methods has been summarised at protocols.io. However, I cannot access it for now. The method description is enough in natural language, but it would be difficult to reproduce the results only by such a description, and I expect that all the necessary information will be uploaded for reproducibility such as the executed environmental information, command arguments, options, and parameters and so on.
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?	Yes
Additional Comments
Any Additional Overall Comments to the Author	In this manuscript, three types of methods for the de novo genome assembly on Melaleuca alternifolia (tea tree) are evaluated. The authors conducted the following three de novo assemblers, 1) Canu, 2) Flye, and 3) MaSuRCA. Only with MaSuRCA, the Illumina short reads which have been published are used together with the newly sequenced PacBio long reads data. Gene annotation was done on the three assemblies by Fgenesh++ in the same manner and conditions. The assemblies and annotations were evaluated with several criteria such as N50 (continuity), BUSCO (single-copy orthologs validation). Then, by using the MaSuRCA result (assembly), comparative genomics analysis was conducted. The assemblies and annotations are overall well explained and examined, and it is worth publishing the assembled genome for the scientific and industrial communities. However, I found some typos and unclear sentences. Please check and correct the following points: * 100 (RRID:SCR_006525) [25], and variants were called using The Genome Analysis Toolkit This must be a typo, "The" should be small letters or it is not needed here. * 151 (. Based on a flow cytometry genome size estimate It is a typo. The period should be out of the brackets, or maybe the bracket should be removed. Please check the following Errors and whether reference sources are correct * 181 scaffolds in the MaSuRCA assembly (Error! Reference source not found.). * 215 of M. alternifolia and E. grandis (Error! Reference source not found.). * 244 other? rosids P. trichocarpa, S. purpurea and V. vinifera (Error! Reference source not found.). * 242 The resulting species tree showed Arabidopsis as outgroup, while the Myrtaceae members E. grandis, C. citriodora and M. alternifolia form a clade that separated from the other? rosids P. trichocarpa, S. purpurea and V. vinifera This sentence is incorrect grammatically. It may be related to this part, and there is no sentence found to refer to Figure 3. Additionally, it would be worth describing which method (e.g. Neighbor-joining, UPGMA, etc.) is used for inferring the phylogenetic tree.
Recommendation	Accept