Bicolor angelfish (Centropyge bicolor) provides the first chromosome-level genome of the Pomacanthidae family

Abstract

The Bicolor Angelfish, Centropyge bicolor, is a tropical coral reef fish. It is named for its striking two-color body. However, a lack of high-quality genomic data means little is known about the genome of this species. Here, we present a chromosome-level C. bicolor genome constructed using Hi-C data. The assembled genome is 650 Mbp in size, with a scaffold N50 value of 4.4 Mbp, and a contig N50 value of 114 Kbp. Protein-coding genes numbering 21,774 were annotated. Our analysis will help others to choose the most appropriate de novo genome sequencing strategy based on resources and target applications. To the best of our knowledge, this is the first chromosome-level genome for the Pomacanthidae family, which might contribute to further studies exploring coral reef fish evolution, diversity and conservation.

The Bicolor Angelfish

**Reviewer 2. Ole K. Tørresen ** Is the language of sufficient quality?
No. Almost every second sentence in the abstract would need work, and so is the rest of the manuscript.

General comments: The authors have created a chromosome-level genome assembly of bicolor angelfish using stLFR and HiC libraries.

The language in this manuscript needs some work. After commenting on every second sentence in the abstract regarding some language matter, I saw that I couldn’t continue commenting all these matters. Please do a good clean-up in the language, so that it is easier to read. I’ll point out some issues during the manuscript, but will not find all and I can’t manage to point out all I do find.

Specific comments: Line 19: «...special and beautiful two-color body” is a bit subjective. Maybe something like “…remarkable and striking two-color body” instead?

Line 20: I know this is the abstract, but I don’t understand what “the mechanism of bicolor body” could mean. Maybe rephrase?

Line 22: I’ve seen this many places, but it should be a lower-case k in kb, not upper case like Kb. The k stands for kilo which is a metric prefix meaning thousand (https://en.wikipedia.org/wiki/Metric_prefix).

Line 25: “As we are known,” should be “as far as we know”.

Line 27: “Future research” instead of “future researches”.

Line 46: Which protocol are you talking about?

Table 1: How can you end up with more “valid data” than “raw data”? Did you mix up something here? It looks consistent with the text, but there’s likely something wrong.

Recommendation Minor Revision

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Abstract

This paper has been reviewed by GigaByte Journal and all peer reviews are shared CC-BY 4.0.

**Reviewer 1. Claudius F Kratochwil. ** Is the language of sufficient quality?
No. The text is understandable, but has many grammatical errors. The manuscript would greatly improve through language editing.

Are all data available and do they match the descriptions in the paper?
Yes. I did not check every single file, but all data I looked for I found to be publicly available. It would help if the "Availability of supporting data and materials" statement would be a bit more comprehensive. Data A is deposited under X, Data B is deposited under Y-Z instead of just providing the project ID.

Are the data and metadata consistent with relevant minimum information or reporting standards? Yes. To the best of my knowledge. Not my area of expertise.

Is the data acquisition clear, complete and methodologically sound?
No. I was lacking information about the transcriptomic data (it says in line 44 that RNA was extracted) that was used for the annotation? Was RNA only extracted from the muscle? Maybe the caveats that go along with that should be discussed. How was the data processed? How many reads etc. I think the manuscript lacks information about this unless I misunderstood where the data for the "transcript-based prediction" came from. Then this should be indicated more clearly.

Is there sufficient detail in the methods and data-processing steps to allow reproduction?
Yes. To the best of my knowledge. I am not an expert on this. Minor comments: l 46: Which protocol?

Is there sufficient data validation and statistical analyses of data quality?
Not my area of expertise. One thing that could be probably additionally done is to provide dot plots with the 1-2 more closely related species with chromosome level assemblies (probably Tilapia or Medaka).

Is the validation suitable for this type of data?
Yes. As far as I can judge the analysis is fine.

Is there sufficient information for others to reuse this dataset or integrate it with other data?
Yes. Genome and annotation are available, which is the most important for reuse and integration with other data sets. So as far as I can judge there is sufficient information for others.

Any Additional Overall Comments to the Author:
From my viewpoint, this is a useful chromosome-level genome, so I support its publication. Beyond being a useful resource, I was however a bit disappointed by the 'scientific part' regarding the bi-color body formation. While the pigmentation of the bicolor angelfish is certainly a very exciting phenotype, the analysis performed is far too superficial to give any solid insights into the phenotype. I would suggest the authors toning this down in title, abstract and main text. It is fine to mention this as a future research direction and to state that the performed initial analysis (fig. 6 and 7) might aid these investigations, but the data does not permit further conclusions. Especially as GigaByte does not focus on analyses for biological findings, this should be completely sufficient.

Recommendation: Major Revision

Re-Review: I am happy with the changes made and thank the authors for addressing them. The manuscript is in my opinion acceptable for publication. Congratulations to the authors for providing a reference genome for this exciting fish species to the community.

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Bicolor angelfish (Centropyge bicolor) provides the first chromosome-level genome of the Pomacanthidae family

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