Reviewer name and names of any other individual's who aided in reviewer |
Mary Ann Tuli |
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.) |
Yes |
Is the language of sufficient quality? |
Yes |
Please add additional comments on language quality to clarify if needed
|
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).
2) 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.
3) 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? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a> |
Yes |
Additional Comments |
Nomenclature standards have been met.
All cited INSDC accession numbers are publicly available.
|
Is the data acquisition clear, complete and methodologically sound? |
Yes |
Additional Comments |
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 |
Additional Comments |
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 |
Additional Comments |
|
Is the validation suitable for this type of data? |
Yes |
Additional Comments |
|
Is there sufficient information for others to reuse this dataset or integrate it with other data? |
Yes |
Additional Comments |
|
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.
Please send the files to us via the FTP server details at the end of this email.
Please note the following.
We strongly recommend filenames are concise and meaningful (e.g. "gene_exp_cell_lines.csv" is better than "Supp1.txt").
Filenames should be unique.
Filenames should not include spaces. We recommend using the underscore (_) in place of spaces in the filenames.
Filenames should only include the following characters a-z,A-Z,0-9,_,-,+,.
Text and tabular information must be in a non-proprietary and text-based format (e.g. CSV/TSV rather than PDF or XLS)
Images must be in a lossless raster format (e.g. TIFF, PNG) or vector format (e.g. SVG).
If you encounter any errors please send us the full context and error message to help us resolve the problem.
username = user34
password = SahacitriChiD
FTP server = parrot.genomics.cn
For using tools like FileZilla use the standard FTP protocol (not sftp).
If you are using command line FTP, you may need to use the passive mode (e.g. use epsv command):
> ftp @parrot.genomics.cn
Connected to parrot.genomics.cn.
220 (vsFTPd 2.0.5)
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> epsv
EPSV/EPRT on IPv4 off.
ftp> put
local: remote:
227 Entering Passive Mode (218,188,108,76,126,77)
150 Ok to send data.
100% |************************************************************************| 12 137.86 KiB/s 00:00 ETA
226 File receive OK.
12 bytes sent in 00:00 (0.26 KiB/s) |
Recommendation |
Minor Revision |