Reviewer name and names of any other individual's who aided in reviewer |
Xu Wang |
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
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Are all data available and do they match the descriptions in the paper? |
No |
Additional Comments |
PRJNA786364 cannot be found at NCBI. The numbat assembly can be assessed at AWS https://threatenedspecies.s3.ap-southeast-2.amazonaws.com/index.html#Myrecobius_fasciatus/. |
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 |
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Is the data acquisition clear, complete and methodologically sound? |
Yes |
Additional Comments |
In this manuscript, Peel et al. sequenced and assembled a draft genome of Myrmecobius fasciatus, a termitivorous marsupial species known as the numbat. A total of 94% sequencing reads could be mapped to the draft assembly, and 96% of RNA-seq reads from three tissues can be aligned. This is the first genome assembly for this species and provides the necessary genome resource for molecular study of the interesting characteristics in this species. |
Is there sufficient detail in the methods and data-processing steps to allow reproduction? |
No |
Additional Comments |
One major concern is the completeness of this assembly. The BUSCO analysis revealed a completeness score of 83%, missing one-fifth of mammalian BUSCO genes. The missing gene models in this assembly may affect the inference of gene gain/loss and gene family expansion. The authors should discuss this, so the audience can be aware of this when using this assembly for comparative genomic analysis.
Please find the specific comments below:
1. To determine whether this assembly is incomplete or not, a genome size estimation analysis should be performed based on K-mers or other approaches.
2. How many chromosomes are their in numbat genome? Could the authors describe the katyotype if it has been characterized in the previous literature?
3. Line 73, 82.8% complete BUSCO: could the authors break this down to single-copy, multiple-copy BUSCOs?
4. Line 95, 10x Genomics does not support genomes larger than the human genome. How much input DNA the authors used for the 10x library prep?
5. Line 190, Table 1: please add the Monodelphis and Tammy wallaby genome assembly statistics, which are the first two assembled marsupial genomes.
6. Line 193, the numbat repeat content (47.6%) was compared to antechinus (44.8%) and koala (47.5%). I suggest that the authors add the two species in Table 2, to check if any specific classes of repetitive elements were enriched in numbat.
7. Did the authors assess the level of potential contamination from microbial species?
8. I suggest the authors talk the top 20 largest scaffolds, and perform a syntenic analysis compared to tammar wallaby or the koala genome.
9. Line 295. Vomeronasal receptors: marsupials have a large number of olfactory receptors. Have the authors check the total number of olfactory receptor genes in the numbat, and how does it compare to other marsupial species?
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Is there sufficient data validation and statistical analyses of data quality? |
Yes |
Additional Comments |
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Is the validation suitable for this type of data? |
Yes |
Additional Comments |
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Is there sufficient information for others to reuse this dataset or integrate it with other data? |
No |
Additional Comments |
PRJNA786364 cannot be found at NCBI. Please release the dataset after acceptance. |
Any Additional Overall Comments to the Author |
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Recommendation |
Minor Revision |