Transcriptome Analysis of Immune Responses and Metabolic Regulations of Chinese Soft-Shelled Turtle (Pelodiscus sinensis) against Edwardsiella tarda Infection
Round 1
Reviewer 1 Report
This is a very interesting paper, and the authors have done a nice job with the data, and communicating the significance of the results. As expected based on the particular disease agent, complement and coagulation pathologies are nicely shown. I do recommend that the authors reach out to an English-writing colleague to modify various sentence structures. Otherwise, this is a nice paper.
Author Response
Dear reviewer,
Thanks for your useful recommendation, we’ve corrected the mistakes of grammar, spellings according to the suggestions of an English-writing colleague.
Reviewer 2 Report
the paper is well structured, with excellent methodological rigor and lays a good foundation for understanding the immune mechanisms also in other reptiles, such as in sea turtles. English would need to be reviewed by a native speaker. I would like to integrated the references with the two citations that I have indicated in the text. Given the important results, I believe that the discussions need to be reformulated following the methodology and the results.
Comments for author File: 
Comments.pdf
Author Response
Dear reviewer,
Thanks for your useful recommendation.
Point 1: We’ve cited and integrated the research articles you’ve suggested as our references with format modification in the MS.
Point 2: Several mistakes of grammar, spellings were corrected according to the suggestions of an English-writing colleague, and explanatory texts about the figures were added.
Point 3: The discussion has been rewritten and deleted several redundant sentences that already existed in the results part.
One problem is that the original data of the Figure 3 were not found, and we’ve been trying contacting with the technological corporation to revise the figure, and it will be uploaded as soon as we finished.
Reviewer 3 Report
Review
Paper title: Transcriptome analysis of immune responses and metabolic regulations of Chinese soft-shelled turtle (Pelodiscus sinensis) against Edwardsiella tarda infection
The authors studied the effects of the pathogenic bacteria Edwardsiella tarda on the immune system of the Chinese soft-shelled turtle Pelodiscus sinensis. The authors provided gene expression profiles in the turtle liver using RNA sequencing and found significant differences between the experimental and control groups. The coagulation cascades pathway, phagosome pathway, and steroid hormone biosynthesis pathway were found to be responsible for the differences in the gene expression profiles indicating that these were mainly associated with defense mechanisms in turtle liver against E. tarda. This process was established to occur on day 4 after infection. These results provide novel information and may have important implications for further research and aquaculture of Pelodiscus sinensis.
All these reasons explain the relevance of the paper by Qianrong Liang Yang and co-authors submitted to "Fishes".
General scores.
The data presented by the authors are original and significant. The study is correctly designed and the authors used appropriate methods. In general, the statistical analyses are performed with good technical standards. The authors conducted careful work that may attract the attention of a wide range of specialists focused on turtle biology, diseases and aquaculture.
Recommendations.
Figure 2. The authors should increase both the font size and resolution.
Figure 3. The text on the OX-axis is too small and hard to read.
Figure 5. The authors should indicate what do vertical bars mean.
The first sentence in the Discussion is difficult to understand. Please, re-write.
L 212-221. This text is redundant and should be deleted.
L 227-235. This text is redundant and should be deleted.
Specific comments.
L 15. Change “bacterium in” to “bacteria”
L 17. Change “profiles in the turtle liver was” to “profiles in the turtle liver were”
L 24. Change “It’s a first time that the gene profile of anti-E. tarda response of soft-shelled turtle was revealed” to “For the first time, we reported the gene profile of anti-E. tarda response in soft-shelled turtle”
L 33. Change “portion in animal protein sources to the” to “portion of animal protein sources to”
L 34. Change “soft-shelled turtle cultivation” to “the soft-shelled turtle cultivation”
L 38. Change “cause” to “causes”
L 39. Change “As is named” to “As it is named”
L 40. Change “accompanied” to “association”
L 45. Change “gram-negative and intracellular bacteria” to “a gram-negative and intracellular bacterium”
L 50. Change “quite a few of” to “quite a few”
L 54. Change “hormone genes” to “and hormone genes”
L 56. Change “could draw” to “can draw”
L 57. Change “have now been” to “has now been”
L 65. Change “Latest research” to “A recent research”
L 67. Change “exprssed” to “expressed”
L 84. Change “average weight” to “an average weight”
L 88. Change “seperated from the suffered with” to “separated from the animals suffered from”
L 90. Change “normal saline” to “normal saline water (or solution?)”
L 90. Change “experiment group” to “the experimental group”
L 92. Change “each was injected” to “were injected”
L 95. Change “after executed to death” to “after being executed to death”
L 102. Change “were analysis of” to “were analyzed using”
L 136. Change “assay of” to “the assay by”
L 146. Change “procedures described as following” to “procedures are described as follows”
L 154. Change “experiment group” to “the experimental group”
L 155. Change “increasingly mortality during” to “an increase in mortality from”
L 156. Change “control group” to “the control group”
L 161. Change “experiment group” to “the experimental group”
L 162. Change “to battle with” to “to battle”
L 163. Change “the experiment group and control group” to “groups”
L 169. Change “differentially expressed” to “differentially expressed levels”
L 179. Change “oxidation-reduction process” to “the oxidation-reduction process”
L 187. Change “group” to “groups”
L 202. Change “Ten of DEGs” to “Ten DEGs”
L 204. Change “showed mainly consistent with” to “were mainly consistent with the”
L 204. Change “a slight differences” to “slight differences”
L 222. Change “experiment group” to “the experimental group”
L 223. Change “to battle with” to “to battle”
L 228. Change “expressed” to “expressed levels”
L 239. Change “a protease complex, including classical” to “the protease complex, including the classical”
L 245. Change “Similarly found in our research,” to “Similarly, we found that”
L 250. Change “one of the inhibitor factor CFH was highly expressed as well” to “the inhibitor factor CFH which was highly expressed”
L 255. Change “coagulation cascades pathway” to “the coagulation cascades pathway”
L 263. Change “bridges” to “bridge”
L 265. Change “urchin” to “sea urchin”
L 271. Change “intracellular and extracellular environment” to “the intracellular and extracellular environments”
L 279. Change “that the phagocytosed” to “where the phagocytosed”
L 305. Change “excessive dose” to “excessive doses”
L 308. Change “hormone level” to “hormone levels”
L 320. Change “might closely associate with” to “might closely be associated with”
L 322. Change “were main genes” to “were the main genes”
Author Response
Dear reviewer,
Thanks for your useful recommendation.
Point 1: The Figure 2 has been revised and the Figure 5 has been added with explanatory texts. One problem is that the original data of the Figure 3 were not found, and we’ve been trying contacting with the technological corporation to revise the figure, and it will be uploaded as soon as we finished.
Point 2: Several mistakes of grammar, spellings were corrected according to the suggestions of an English-writing colleague.
Point 3: The discussion has been rewritten and deleted several redundant sentences that already existed in the results part.
The revised manuscript has been attached.
