In silico characterization of chitin deacetylase genes in the Diaphorina citri genome

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1. 

   GigaByte

   Sep 12, 2021

   Now published in Gigabyte doi: 10.46471/gigabyte.25

   This work has been peer reviewed in GigaByte (https://doi.org/10.46471/gigabyte.25), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

   Reviewer 1. Xingtan Zhang and Yingying Gao

   The manuscript entitled “Characterization of chitin deacetylase genes in the Diaphorina citri genome” has an interesting subject. However, general organization and content of the manuscript is not well developed and needs extensive revision. It seems to me that the introduction does not offer a good amount of useful information or background knowledge for its reader. Some sentence is confused (as example see line 30).

   The topic " Materials and Methods" Lines 137-139. For the software, which one was used or both as there is only one tree plot? …

   Now published in Gigabyte doi: 10.46471/gigabyte.25

   This work has been peer reviewed in GigaByte (https://doi.org/10.46471/gigabyte.25), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

   Reviewer 1. Xingtan Zhang and Yingying Gao

   The manuscript entitled “Characterization of chitin deacetylase genes in the Diaphorina citri genome” has an interesting subject. However, general organization and content of the manuscript is not well developed and needs extensive revision. It seems to me that the introduction does not offer a good amount of useful information or background knowledge for its reader. Some sentence is confused (as example see line 30).

   The topic " Materials and Methods" Lines 137-139. For the software, which one was used or both as there is only one tree plot? Why these species were chosen?

   Some useful experiments targeting the genes need to be conducted further. The data from RNA-seq should be confirmed by other experimental methods to support your result or conclusion. The results and conclusion are less informatic, and discussion is missing. The manuscript feels more like an informal work report rather than a research article.

   Figures and tables also need extensive revision. The figures and tables are important, but the figures and tables titles could be more descriptive and clear. And the notes of them should be separated from the title so that it can be more readable. Particularly, as a “note”, useful information in the figure needs explanation instead of repeating of method. Make sure the formats of all tables are consistent.

   The references could be improved (increase the number of references). There are many formatting mistakes, please check. It is fundamental to understand basic rules of reference, please review all them after that.

   **Reviewer 2. Mary Ann Tuli ** Is the language of sufficient quality?
   Yes. 1) Line 27. "Genomic" should be "genomic"

   Are all data available and do they match the descriptions in the paper?
   No. Additional Comments: 1) Line 137. "Multiple alignments were performed using MUSCLE " We need the output of MUSCLE (FASTA).

   1. Line 137. "phylogenetic trees were constructed (figures 1 and 3) in MEGA7 or MEGAX." We need the files underlying the phylogenetic tree (newick). Please indicate which version of MEGA was used for each tree.

   2. Line 139. "Expression data from CGEN was visualized using the pheatmap package of R or Microscoft Excel" Please can you provide a file of the raw data used to produce the heatmap (figures 2a ) and the TMP graph (figure 2b).

   Are the data and metadata consistent with relevant minimum information or reporting standards? Yes. Nomenclature standards have been met. All cited INSDC accession numbers are publicly available.

   Is the data acquisition clear, complete and methodologically sound?
   Yes. The curation workflow used for community annotation is available via protocols.io , nonetheless the manuscript includes a comprehensive summary which is appropriate.

   Is there sufficient detail in the methods and data-processing steps to allow reproduction?
   No. See "Are all data available and do they match the descriptions in the paper?" above. Once the additional files are made available I believe reproduction will be possible.

   Is there sufficient data validation and statistical analyses of data quality? Yes

   Is the validation suitable for this type of data? Yes

   Is there sufficient information for others to reuse this dataset or integrate it with other data? Yes

   Any Additional Overall Comments to the Author:

   1. Citation [23] MUSCLE. https://www.ebi.ac.uk/Tools/msa/muscle/.

   • the website suggests users of MUSCLE cite DOI:10.1093/nar/gkz268

   Some of my comments/recommendations are pertinent to the other D. citri manuscripts currently under review.

   Read the original source
2. Version published to 10.46471/gigabyte.25

   Jun 11, 2021
3. 

   Version published to 10.1101/2020.12.22.424074v1 on bioRxiv

   Dec 22, 2020