Transcriptome Analysis Provides an Overview of Genes Involved in the Peculiar Food Preference at First-Feeding Stage in Mandarin Fish (Siniperca chuatsi)
Round 1
Reviewer 1 Report
Dear Editor,
The manuscript entitled “Transcriptome analysis provides an overview of genes involved in the peculiar food preference at first-feeding stage in mandarin fish (Siniperca chuatsi)” by Ling Li et al. presents the comparative transcriptome analysis of mandarin fish larvae fed under 3 conditions: (1) unfed; (2) fed with live prey fish and (3) fed with brine shrimp (Artemia). The authors report that differential expression of transcription factors involved in retinal photoreceptor development and differentiation might contribute to the intake of brine shrimp in mandarin fish larvae, and digestive enzyme genes involved in protein, fat and carbohydrate digestion have been expressed in mandarin fish larvae at first-feeding stage.
Τhe manuscripts’ objects are quite interesting, the manuscript is well-written and could be accepted for publication after major revisions. My detailed comments for the authors to consider are provided below:
1. Critical confirmation of selected genes expression profiles by RT-PCR is totally missing. Until provided all conclusions are speculative.
2. The discussion is very descriptive and not placing the present work findings under a specific perspective.
3. Discussion of GO and KEGG categories differentiation among the studied conditions would be beneficial.
4. The supplementary files were not provided.
5. Page 1, lines 33 and 35: Please specific references.
6. Page 3, section 2.1: have the authors used 3 biological replicates per tank? Please specify.
7. Y-axis legends in GO and KEGG tables in figures 2,3,4 are not readable.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The proposed manuscript (ms) “Transcriptome analysis provides an overview of genes involved in the peculiar food preference at first-feeding stage in mandarin fish (Siniperca chuatsi)” greatly contributes to the study of evolutionary biology, especially how exogenous feeding influences gene expression and organ development. This study nicely shows ongoing evolution and how body development is influenced by feeding factors. The ms is technically sound, presented in an intelligible fashion and written in good-quality English. Impact of the study is well highlighted. I appreciate the wide range of methods (RNA extraction, library preparation, NGS, data and statistical analysis, gene expression). On the other hand, the main discrepancy of the ms is that sex of animals is not taken in account.
After overall consideration of the manuscript quality I suggest major revision. After following the above recommendations, the manuscript can meet the requirements of the Fishes journal.
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Differential gene expression might be found between males and females. Why authors did not identified sex of fish? It must be explained and reasoned within the ms.
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Abbreviations in the text are not explained after the first use (e.g. DEGs), and some abbreviations are explained more times (e.g. dph). In the abstract, plain text and first figure description, authors have to explain each abbreviation separately.
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Check italics in each scientific name (e.g. row 142)
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Gens is probably a typo (row 149)
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Another important point is that the mandarin fish do not accept non-fish live feeds. But the experimental fish were fed with brine shrimp. There is no explanation how authors reached that experimental mandarin fish feed on non-fish live feed.
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I recommend minor linguistic revision, especially the usage of definite articles.
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I do not see any supplements. Was the supplementary material submitted?
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Authors followed all recommendations and the proposed manuscript was improved. I am looking forward to seeing the published version of the paper.
