The QUBES MRA resources was hugely helpful for our past two MRA submission.  I received this comment from our last submission: "Each accession number reported in the manuscript must be hyperlinked to the publicly available data record."  Might also be good to have as reference the MRA checklist before submission to make sure authors include all of the details they are looking for: https://journals.asm.org/pb-assets/pdf-text-excel-files/MRA-Author-Checklist-1659729670130.pdf

The MRA Resource, combined with the quick turn around of feedback from the Internal Review was great.

We annotated two genomes from the Genome Exchange.

MRA 1 : The reviewer commented that the paper was in a pretty good shape and asked for the following:

• To share the TEM image
• To include a description of software used for Illumina read sequence read quality control, error correction and adapter trimming
• To state the genes as putative

MRA 2 : Some comments from a different Reviewer:

• To specify the date which the sampling was performed
• To give a range for the number of plaque purification performed per phage
• Auto-annotations should be stated as Automated Annotations
• Annotations of genes should ideally identify as putative

We had two MRAs, both written by students, one edited by me and one edited by Ivan. The editors were different, and from their styles the reviewers were likely different as well.

Both asked for the SRA snd GBK links to be moved from a separate paragraph back into a table. I don't know if they all prefer that since it was suggested that we do the oposit, but that's what ours prefered. It may be luck of the draw. Both also had us cut down the additional reasearch we added as a figure a bit. Here are pretty much all of the details.

MRA 1 (Cluster BI phages) -

• Move SRA and GBK information from separate paragraph to the included table
• Addition of software used for end determination and GCS
• A couple minor (good) adjustments like the addition of "predicted" and a clarification of wording
• Simplification of Figure, they felt it was a little repetative. We cut it from three to two panels and adjusted the text accordingly

MRA 2 (Cluster BF phages) -

• Move SRA and GBK information from separate paragraph to the included table
• Addition of software used for GCS determination
• Addition of micrographs if possible
• Addition of plaque sizes (which seemed like a oddly trivial request to me)
• Simplification of Figure, they felt panel A was covered in the text. They also wanted some additional explanation of the methods for panel B. We replaced panel A with micrographs to correct the above request and added the needed explanation.

Overall, not too many changes.

Steve

The reviewer for our submission requested additional information:

1. Include databased used to mine HHPred and BLASTp.

• HHPred: PDB_mmCIF70, SCOPe70, Pfam-A, NCBI_Concerved_Domains (CD)
• Blastp: Actinobacteriophage Proteins, non-redundant protein sequences (nr)

2. Indicate how gene similarities were determined (same as Ellen Wisner's comment).

• Cluster assignment was determined based on clustering parameters of at least 35% shared protein homologs (phams) to others in the same cluster in the Actinobacteriophage database. (Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, Russell DA, Warner MH, Science Education Alliance-Phage Hunters Advancing G, Evolutionary S, Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8.)

This resource was great, without it we would not have been able to publish our MRA.

We have a unique situation as the phage we annotated was from the Genome Exchange, as a result we had to reach out to the institution that did the isolation for a lot of information about the isolation of the phage.  This was fine as they had great notes and responded quickly, but got me thinking that perhaps all of that information (the info required for an MRA) could be included somewhere on phagesdb.  Below I have listed all of the extra information (that wasn't already on PhagesDB) that we had to get from the discovery/isolation team:  

• Media Type (ex: PYCa) -
• How many days was the enriched culture was incubated?
• Plaque Purification Incubation Time -
• Rounds of Purification -
• DNA isolation kit used - 
• Pore size of filter used for isolation - 

We felt like the review process went pretty well.  This is what the reviewer had us change/suggestions:

• They wanted us to include the micrograph, however, unfortunately, it didn't meet the DPI requirements. 
• Please state from what sample DNA was isolated, a phage lysate, confluent lawns, CsCl purified virions, etc.
• Were reads quality controlled in any way, if so please state which software was used to do so.
• Anytime we referred to a particular gene with a function they had us add in "predicted" as these had not yet been experimentally tested.
• We mentioned that our phage was assigned to a subcluster based on a a gene content similarity of >35%.  They requested "Please state how this gene content similarity was determined."  In order to save space in our paper, we changed this to "Tokki is classified as a subcluster AU2 bacteriophage using previously described criteria" and cited phagesDB and Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, Russell DA, Warner MH, Hatfull GF, Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES). 2017. Bacteriophages of Gordonia spp. display a spectrum of diversity and genetic relationships. mBio 8:e01069-17.

I just wanted to share a couple of tips about the MRA submission process:

• If the corresponding author is the submitter to MRA, the process is smoother. I made the mistake of  submitting the article with another author as the corresponding author. This caused some difficulties in the system when trying to sign the “Author Warranty and Provisional License to Publish” electronic form.
• Include a comment in the “Page Charges” comment box that this paper has a pre-negotiated fee of $150.
• If you need to make modifications to the submission based on reviewer’s comments, the modified text file should be uploaded as a word text or equivalent (not a pdf).
• The modified submission is not a new submission (there are 2 boxes, but it’s a little confusing since “modified submission” isn’t an option; just don’t check the “new submission” box!)

Reviewers may ask to add to manuscript the date at which the phage sample was taken and GPS 

Having others in the SEA read and comment on our manuscript was enormously helpful! And having the workflow got us over the "activation energy" we needed to submit our first manuscript. We have a second one that has been accepted since so apparently the activation energy was truly lowered :).

Some comments we got from reviewers and other advice:

1. We needed GPS coordinates to be more precise. I truncated them because I thought it looked better. Don't do that.

2. We needed to clarify the use of Newbler and Consed and to let them know how the genome ends were determined.

3. We needed to include "putative" or "predicted" with all our functional calls.

4. Include staining method for TEMs.

5. Reviewers said due to ICTV revision, Siphoviridae is no longer being used. Suggested using "siphovirus morphology".

6. Include whether soil samples were from surface and volume of soil used in isolation.

7. One reviewer wanted the total reads for each phage so I included that in our table.

8. I had some trouble at first getting our plaque pictures to have the correct resolution. I used this online converter and it worked well: https://image.online-convert.com/convert-to-tiff

9. Give yourself some nice, uninterrupted time to do the submission. It took me longer than I thought it would.

Thanks to the team (especially Vik!) for your help!

Hi, on the checklist, it would be good to include that the accession numbers and software URLs need to be hyperlinked.  MRA has that on their checklist and I missed it the first time.