Linking Fungal Genomics to Thermal Growth Limits: A Dataset of 730 Sequenced Species

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The paper deals with a methodology to evaluate existing genomic and temperature data for fungi. The paper is interesting in the fact that it utilizes existing accessible data sets for its analysis.

The main issue with the paper is in the methods section. They are referenced to previous publications, but they are not described in detail. A recommendation for the authors is to extend this section with further detail. For example, the Togashi analysis referenced in the paper is not well explained and is hard to understand why is it part of the data analysis.

Comments on the Quality of English Language

The summary section is written in the first person, when it is standard for scientific research to have it in the third. It is recommended to edit that section.

Author Response

Comments and Suggestions for Authors

The changes in the manuscript are marked in red, for ease of tracking the new text.

Referee #1

The paper deals with a methodology to evaluate existing genomic and temperature data for fungi. The paper is interesting in the fact that it utilizes existing accessible data sets for its analysis.

I thank the reviewer for this supportive comment.

The main issue with the paper is in the methods section. They are referenced to previous publications, but they are not described in detail. A recommendation for the authors is to extend this section with further detail. For example, the Togashi analysis referenced in the paper is not well explained and is hard to understand why is it part of the data analysis.

I have expanded the Methods section considerably. I have not gone into deep technical detail about how Kogo Togashi compiled his book, as I do not know (and he died in 1952, so I cannot ask him!)

Comments on the Quality of English Language

The summary section is written in the first person, when it is standard for scientific research to have it in the third. It is recommended to edit that section.

This is an old trope, and one that ignores both modern practice and the undisputed fact that science is carried out by people, not abstractions. To write “A search was conducted” rather than “I conducted a search” gives the paper a spurious sense of institutional authority that is at odds with reality. In any case, modern scientific writing uses personal pronouns extensively.  As evidence, and in response to exactly this comment addressed at a previous paper, I looked at the main text of primary research papers (not reviews, op-eds, news pieces etc) in issues of Science (VOLUME 383|ISSUE 6681|26 JAN 2024), Nature (Volume 625 Issue 7996, 25 January 2024), and New England Journal of Medicine (Feb 8^th 2024). I looked for constructions such as “We examined” or “We demonstrate” “Our research” rather than “This study tested” or “It was demonstrated” or “This research”. In Nature, 16 out of 22 articles used active first person voices (and another two mixed active and passive, for example saying “We sorted peripheral cells … These clusters were assigned”). In Science 6 were first person, one third person passive and five mixed. NEJM, perhaps because the articles were all reporting patient outcomes, were more impersonal with 1 third person and three mixed papers.  All parts of the first person papers were first person, not just reporting procedures, as illustrated by phrases such as “Here we take a step forward” “We hypothesise” “Our model” “We reasoned”  “We opted to investigate” “To test our first prediction” “We consider” “We are conducting this phase 3 trial” “Here we report”  “we measured” “we laser cool an ensemble …” “we demonstrate” “We confirmed” “We conclude” just to quote a few at random.

This is not a modern phenomenon: anecdotally, I note that Watson and Crick (1953) starts with the word “We”.

None of these papers say “I” because they are all multi-author papers. However they use the first person active voice. I have therefore tried to reduce the number of times I say ‘I’, but I have *not* rewritten the section to avoid the personal pronoun completely. If this violates MDPI editorial policy then the paper will be rewritten accordingly, but in that case it is strongly considered that the journal policy be changed by the editor.

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Author,

Thank you for sharing this dataset and Excel program. I find it very interesting and believe it could be valuable to other researchers. I have added comments in both documents. In the Excel file, they are additionally highlighted with yellow cell coloring or red font to make them easier to locate.

All the best!

Comments for author File: Comments.zip

Author Response

The changes in the manuscript are marked in red, for ease of tracking the new text. 

Referee #2

Thank you for sharing this dataset and Excel program. I find it very interesting and believe it could be valuable to other researchers. I have added comments in both documents. In the Excel file, they are additionally highlighted with yellow cell coloring or red font to make them easier to locate.

I think the reviewer for this, and for their detailed and helpful comments on the MSS and the excel file.

Comments from MSS

I think the title is not the most representative for the manuscript. I suggest some corrections. Maybe something in line: Linking Fungal Genomics to Thermal Growth Limits: A Dataset of 730 Sequenced Species

I like this title! Thank you, I have adopted it.

Line 26. at about?

Apologies, this is a typo, it should be ‘above’. Now corrected.

Line 47 what is meant by that?

 I have reworded this

Line 47-48 which project?

The one reported in this paper, but I have reworded.

Line 52 is there a need for use of double brackets?

No, here and elsewhere odd reference formatting is an artefact of the citation software. I have changed this in the revised version.

Line 54 in Table 2?

Yes – added Table 2.

Line 58 Not 730 as stated in Abstract?

My apologies, there is some mix-up between versions! I have corrected all the numbers, made sure they are consistent, and been more specific with terms like ‘a few’. In this specific instance, it is 699 (not 700) fungal species.

Line 60 specific

corrected

Line 70 order numbers, and is there need for double brackets?

As above – reference software (which is my fault – I should have corrected this before submission).

Line 77 use the same number everywhere

Corrected, as above.

Line 78 add number

done

Line 83 Read Me

Corrected

Table 1. Line under SPECIES is too much. + Can't find this web page

I do not know why that extra line is there – I think it hsq something to do with the table breaking over the page. When I push the table onto the next MSS page, the extra line goes away, but then one appears under ‘Taxonomy’. I hope that MDPI’s publishing group can sort this template snafu. I have corrected the web reference.

What is meant by "combined"?

 This is explained in the Methods section, but I have made this clearer here too

bold the line under Taxonomy

done

Line 108 Introduce the abbreviation

Done

Line 135 SAR is normally written as Sar

Corrected

Line 137 Incorrect spelling and missing capital letter. Pezizomycotina

Corrected

Line 148 (Table 3) Different fonts used in the table

Corrected

Lines 155-6 I would suggest some rephrasing to increase clarity of this sentence. What precisely do you mean by "here the growth of mycelia"

I have rephrased this.

Line 198 please name the constants

These are arbitrary. I could rename them ‘Ab’, ‘B’, ‘C’ etc if that makes it clearer? I have stated that they are arbitrary.

Line 199 centigrade is an old fashioned name for Celsius, please use SI units

Alas, the author hereby reveals themselves to be old fashioned too - corrected

Line 210 combine with the line 201-202

Good suggestion, thank you. Done.

Line 242, 251,  I suggest adding axis titles in the figure

Have done this.

 

Excel spreadsheet.

I have changed ‘thru’ for : notation. I hold that Excel *is* dumb, but appreciate that for a scientific reference data set this might be an unnecessarily personal opinion, and have removed the comment! I have corrected capitalization on the main data sheet. I note that the names as given in the 'Togashi database' sheet of the file which the reviewer highlit in yellow for their lack of capitalization are taken directly from the Dryad sourced database - they are listed there without capitalization. So I have not changed this - I have changed the title of this column to make this clear. 

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript "A dataset of genomic and growth temperature data for fungi" collates data from the literature to present a systematic overview of temperature limits and genomic data availability of fungi across the whole kingdom. This dataset is very useful for future use and the manuscript highlights potential limits of the work neatly.

I only have a few minor points which should be addressed:

• L31: "limits of complex life on other worlds" is a bit of a stretch and I would remove this. Is far more complex than just temperature.
• L38 "opportunistic" not all fungi are, so would just say pathogens
• L39-40 "adapting to higher temperature" C. albicans does not really adapt as it is a commensal. Reword.
• L42-45 needs a ref. Has been reviewed by Van Rhijn & Bromley, Nnadi & Carter and Seidel et al.
• L51 "decade-long in vitro evolution experiments" actually in vitro evolution can be assessed much more rapidly. Reword to show that in vitro evolution works on shorter timescales.
• L93 "complete genome sequence" many of the fungi here do not have complete genomes. Perhaps define what a complete genome is for this purpose.

Author Response

The changes in the manuscript are marked in red, for ease of tracking the new text. 

The manuscript "A dataset of genomic and growth temperature data for fungi" collates data from the literature to present a systematic overview of temperature limits and genomic data availability of fungi across the whole kingdom. This dataset is very useful for future use and the manuscript highlights potential limits of the work neatly.

I think this reviewer for this positive comment.

I only have a few minor points which should be addressed:

• L31: "limits of complex life on other worlds" is a bit of a stretch and I would remove this. Is far more complex than just temperature.
• I agree, but this was an important motivation for the work, so I have down-played the importance of temperature as a limit on complex life, but retained the reference.
• L38 "opportunistic" not all fungi are, so would just say pathogens
• This was specifically addressing fungal species, it was not meant to describe all opportunistic pathogens. I have reworded this to try to make this clearer.
• L39-40 "adapting to higher temperature" C. albicans does not really adapt as it is a commensal. Reword.
• I have reworded to make the adaptation argument clearer.
• L42-45 needs a ref. Has been reviewed by Van Rhijn & Bromley, Nnadi & Carter and Seidel et al.
• Thank you for pointing me to these references, which I have included.
• L51 "decade-long in vitro evolution experiments" actually in vitro evolution can be assessed much more rapidly. Reword to show that in vitro evolution works on shorter timescales.
• It certainly can, and many in vitro evolution experiments have shown exciting results over months, or even weeks, although the classic Lenski series has indeed been running decades, and has shown some of its results only because of this longevity. The very limited work looking at changing temperature optima substantially have taken much longer, and I fear may take a decade or more. However I accept that this is my speculation, and have re-worded, and cited the only such experiment that I know of.
• L93 "complete genome sequence" many of the fungi here do not have complete genomes. Perhaps define what a complete genome is for this purpose.
• I have been more specific about the genome sequence data criteria, specifically that a substantially complete genome sequence was available either as a draft sequence in the literature or on the NCBI or JGI databases.

 

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The paper has been significantly improved. The information in the method sections is way better, and the paper is now written in the correct scientific manner.