Full-Length Transcriptomics Reveal the Gene Expression Profiles of Reef-Building Coral Pocillopora damicornis and Symbiont Zooxanthellae

Round 1

Reviewer 1 Report

I have read the manuscript by Guo et al. in which they use a full-length sequencing approach to explore the expression profiles of the reef-building coral Pocillopora damicornis and its algal symbionts. The authors identify a suite of highly-expressed genes in both the coral host and algal symbiont and discuss the functional features of these genes and their potential role in holobiont maintenance. Overall, I feel that the topic is an interesting one and that the authors have conducted a robust bioinformatic study with important results for the field. However, I identify a few points which I believe necessitate additional consideration before publication. In particular, the Methods section needs to be significantly expanded as it is currently lacking in important details on how the corals were kept and how RNA was extracted from the coral tissue. In addition, the Discussion could be expanded to better incorporate what is already known about the P. damicornis holobiont as well as to more fully describe the links between host and symbiont high-count genes.

 

General Comments:

In general, I believe the manuscript would benefit from additional revision of the text, particularly with respect to grammar. I have tried to note specific areas of concern in my comments below, but would encourage the authors to pass a careful eye over the entire  manuscript. In addition, I have concerns regarding aspects of the experimental design and interpretation of data that I feel need clarification. More specific comments follow below:

 

Specific Comments:

Abstract

Line 14: Suggest changing “tolerant limitation” to either “tolerance limit”.

Line 16: Add “a” after “of” (… of a scleractinian coral …).

Lines 20-22: I feel this sentence could be rewritten to better clarify what data were used/obtained in this study. Also, I believe the number of host genes should be larger than 21. Perhaps reword something like: “To this end, we identified 21,926 and 465 unique genes in the coral and algal symbiont, respectively, and examined functional enrichment among these genes based on GO (Gene Ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways.

Line 23: Change “it” to “their”.

Line 40: As written, this seems to suggest that the common name of Pocillopora damicornis is “stony coral” when it is actually “lace coral” or “cauliflower coral”. I believe the authors mean to say that P. damicornis is a small-polyped stony coral rather than list a common name. Thus, I suggest to use the more clear term “scleractinian coral” in place of “stony coral” here and throughout the paper.

Line 42: Change “Stony coral” to “Scleractinian corals”. In addition, this sentence needs to be re-written because it conveys two (unrelated) ideas: (1) that scleractinian coral population structure reflects their mixed mode of reproduction, and (2) that scleractinian corals contain micro-algal symbionts. These are both true facts, but I don’t think the first point is relevant for this manuscript.

Line 50:  Add “the” between “of” and “symbiont”.

Line 51: Add “that” between “shows” and “the”. Change “express” to “expresses”.

Lines 53-57: This sentence is very long and lists many different types of studies. Suggest splitting this sentence into smaller parts with a more focused discussion of similar studies.

Lines 85: Change “symbiosis” to “algal symbiont”.

 

Methods

Section 2.2 - Lines 94 - 102: More detail is required in this section. Although the authors do a good job of listing the equipment used, this information alone does not provide any detail on the actual conditions the coral experience. What was the volume RedSea 575 aquarium? How many coral fragments were kept together? What is the intensity of the light provided by the AI®, Red Sea Aquatics lamps? What temperature was the coral maintained at? Salinity? etc. As written there is not enough information provided for this experiment to be replicated.

Section 2.3 – Lines 104 -110. This section also needs significantly more detail. How was RNA extracted from the coral? Were coral flash-frozen in liquid nitrogen and then crushed, or was tissue removed by pressurized water, etc? Again, as written, this experimental procedure could not be reproduced because no detail is given about how RNA was extracted from the coral tissue.

 

Discussion

The authors have done an excellent job listing and describing the various genes that were most enriched within the coral and symbiont. However, the manuscript would benefit from a more synthetic approach in which these genes are discussed in regards to the ecology and/or physiology of the holobiont pair. Are there any connections between the host and symbiont in terms of biochemical pathways? Etc.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

The content of the ms is interesting. I could not find any major flaws in the experimental design and implementation. However, additional efforts to improve the presentation of results and discussion would be appreciated. 

Author Response

Please see the attachment.

Author Response File: Author Response.docx