Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial
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Abstract
The numbat (Myrmecobius fasciatus) is an endangered Australian marsupial, and the last surviving member of the Myrmecobiidae family. The numbat regularly undergoes torpor and is unique amongst marsupials as it is the only diurnal and termitivorous species. Here we sequenced the first draft genome of the numbat using 10× Genomics Chromium linked-read technology, resulting in a 3.42 Gbp genome with a scaffold N50 of 223 kbp. A global transcriptome from liver, lung and tongue was also generated to aid genome annotation, identifying 21,465 protein-coding genes. To investigate adaptation to the numbat’s termitivorous diet and arid/semi-arid range, we interrogated the most highly expressed transcripts within the tongue and manually annotated taste, vomeronasal and aquaporin gene families. Antimicrobial proteins and proteins involved in digestion were highly expressed in the tongue, alongside umami taste receptors. However, sweet taste receptors were not expressed in this tissue, which combined with the putative contraction of the bitter taste receptor gene repertoire in the numbat genome, may indicate a potential evolutionary adaptation to their specialised termitivorous diet. Vomeronasal and aquaporin gene repertoires were similar to other marsupials. The draft numbat genome is a valuable tool for conservation and can be applied to population genetics/genomics studies and to investigate the unique biology of this interesting species.
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numbat
**Reviewer 2. Xu Wang **
Are all data available and do they match the descriptions in the paper? No. 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/.
Is the data acquisition clear, complete and methodologically sound? Yes. 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 …
numbat
**Reviewer 2. Xu Wang **
Are all data available and do they match the descriptions in the paper? No. 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/.
Is the data acquisition clear, complete and methodologically sound? Yes. 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. 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?
Is there sufficient information for others to reuse this dataset or integrate it with other data?
No. PRJNA786364 cannot be found at NCBI. Please release the dataset after acceptance.
Recommendations: Minor revision.
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Abstract
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.47), and has published the reviews under the same license. These are as follows.
Reviewer 1. Charles Feigin (reviewer), Elise Ireland (assisted in proofreading)
Are all data available and do they match the descriptions in the paper? I selected "yes" to the question "Are all data available and do they match the descriptions in the paper?" as the genome, annotation, transcriptome etc are currently available through the author's institutional/consortium AWS link. However, so far as I can tell the BioProject number they provide is not yet public. This would contain the same data, but a release in the public repository is a more secure way ensure data is permanently accessible to the community.
Is there sufficient detail …
Abstract
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.47), and has published the reviews under the same license. These are as follows.
Reviewer 1. Charles Feigin (reviewer), Elise Ireland (assisted in proofreading)
Are all data available and do they match the descriptions in the paper? I selected "yes" to the question "Are all data available and do they match the descriptions in the paper?" as the genome, annotation, transcriptome etc are currently available through the author's institutional/consortium AWS link. However, so far as I can tell the BioProject number they provide is not yet public. This would contain the same data, but a release in the public repository is a more secure way ensure data is permanently accessible to the community.
Is there sufficient detail in the methods and data-processing steps to allow reproduction? No.
I have requested in my comments for a few program version numbers, parameters, sequence accession numbers to be included and suggested a few points of clarification on the methods. This should be very straightforward for the authors to address.
Recommendation: Minor Revisions
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