What Do We Know about Botryosphaeriaceae? An Overview of a Worldwide Cured Dataset

Round 1

Reviewer 1 Report

a very interesting work, with an original and complete approach, the paper is well written and clear and I think  the proposed database could be a real useful tools for future research.   No remarks, only a suggestion to modify fig 7 where the axis are not well readable.

Author Response

Reviewer #1: a very interesting work, with an original and complete approach, the paper is well written and clear, and I think the proposed database could be a real useful tools for future research.   No remarks, only a suggestion to modify fig 7 where the axis is not well readable.

Response: The authors are grateful for the acknowledgement of the work done. A new figure was added to improve the reviewer suggestion.

Reviewer 2 Report

The forest manuscript-1129411, titled "What we know about Botryosphaeriaceae? - Overview of a worldwide cured dataset", by 
Batista et al., Presents the creation of a curated database populated with Botryosphaeriaceae data recovered from both NCBI 
and US National Fungus Collections, accessible via a web interface and the results obtained from data mining.
The authors are presenting a nice piece of their research, which could be of interest to a wide audience, in particular because it could be used as a model for similar platforms focused on other biological subjects.
However, there are some points that in my opinion should be perfected.
1. Are the authors available to release their code? If so, they should indicate a repository (GitHub) for free access.
2. There are some procedural steps which are not clear or not completely detailed: 
the identification of duplicates is not clear: on the base of sequence? of metadata? 
all R functions and packages used should be stated along with their version (this is required for research reproducibility), 
e.g. geographical transformation, CHELSA query, etc.
3. Did the Author considered to check genus/species boundaries consistency performing clustering, besides pairwise blast 
searches with the type of each Genus? For example, see clustering used in UNITE ( Nilsson RH, Larsson K-H, Taylor AFS, 
Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K. 
2018. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. 
Nucleic Acids Research, DOI: 10.1093/nar/gky1022) or MaarjAM (Öpik, M., Vanatoa, A., Vanatoa, E., Moora, M., Davison, J., 
Kalwij, J.M., Reier, Ü., Zobel, M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns 
in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188: 223-241). This may lead to the identification of 
outliers refine the species concept in  Botryosphaeriaceae.
4. How the US National Fungus Collections was queried? manually? via API scripting? all those steps should be better explained
5. There are several phrases in the manuscript (line 139, line 257, line 290-91) which give rise to the idea that modeling analyzes have been done to support these claims. I suppose this has not actually been done, and therefore such claims should be reviewed and softened. On the contrary, all modeling procedures should be reported.
6. paragraph 8. Don't forget species substitution by species with better fitness, unless you mean it in point (5), but the concept has to be expanded.
7. paragraph 10. An approximate scheduling of the database update must be provided.
8. Data availability, include code.
9. About the site, 
    . It would  be useful to have the direct link to NCBI clicking on accessions.
    . For each entry I discovered not all the markers were available; the sentence at line 61 must be clarified.
    . In my opinion, the climate data tab might be dropped and data embedded in geographical tab. In fact, it's a bit confusing always having the table above the picture with all the entries, and the user has to search for the species. It would be better if the records from the specific species appear after the selection by user, in Geographical tab.

Author Response

Reviewer #2: The forest manuscript-1129411, titled "What we know about Botryosphaeriaceae? Overview of a worldwide cured dataset", by Batista et al., Presents the creation of a curated database populated with Botryosphaeriaceae data recovered from both NCBI  and US National Fungus Collections, accessible via a web interface and the results obtained from data mining.
The authors are presenting a nice piece of their research, which could be of interest to a wide audience, in particular because it could be used as a model for similar platforms focused on other biological subjects.
However, there are some points that in my opinion should be perfected.

Response: The authors are grateful for the acknowledgement of the work done.

Reviewer #2: Are the authors available to release their code? If so, they should indicate a repository (GitHub) for free access.

Response: The authors are available to release the code regarding data extraction. And a GitHub repository (https://github.com/Batis007/MDRBOT) was created to allow the community to discuss and access both code and source data. However, the process of data cleaning was performed manually and therefore was not possible to prepare a pipeline in R to facilitate the process. Also, through the shinny application it will be possible after publication to download the source data as csv file.

Reviewer #2: There are some procedural steps which are not clear or not completely detailed: 
the identification of duplicates is not clear: on the base of sequence? of metadata? 
all R functions and packages used should be stated along with their version (this is required for research reproducibility), 
e.g. geographical transformation, CHELSA query, etc.

Response: The identification of duplicates was based on metadata using the function unique() from base R. Additional cases detected manually were also removed. The package used for geographical thinning was added in figure 7 caption. All used packages version is stated on GitHub.

Reviewer #2: Did the Author considered to check genus/species boundaries consistency performing clustering, besides pairwise blast searches with the type of each Genus? For example, see clustering used in UNITE (Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K.  2018. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, DOI: 10.1093/nar/gky1022) or MaarjAM (Öpik, M., Vanatoa, A., Vanatoa, E., Moora, M., Davison, J., Kalwij, J.M., Reier, Ü., Zobel, M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188: 223-241). This may lead to the identification of outliers refine the species concept in Botryosphaeriaceae.

Response: We did not consider checking genus/species boundaries consistency performing clustering, as in the studies mentioned. In the Botryosphaeriaceae family different multi locus analysis is used for different genera. Also, it has been demonstrated by several authors that clustering analyses like UNITE exclusively performed based on ITS are not sufficient to delimit species boundaries in this family. (e.g., 1. Phillips, A.J.L.; Alves, A.; Abdollahzadeh, J.; Slippers, B.; Wingfield, M.J.; Groenewald, J.Z.; Crous, P.W. The Botryosphaeriaceae: genera and species known from culture. Stud. Mycol. 2013, 76, 51–167, doi:10.3114/sim0021. or 17. Dissanayake, A.J.; Phillips, A.J.L.; Li, X.H.; Hyde, K.D. Botryosphaeriaceae: Current status of genera and species. Mycosphere 2016, 7, 1001–1073, doi:10.5943/mycosphere/si/1b/13)

Reviewer #2: How the US National Fungus Collections was queried? manually? via API scripting? all those steps should be better explained.

Response: At the moment, it is not possible to query the US National Fungus Collections via API scripting. Queries should be performed internally by the staff of the US National Fungus Collections. As mentioned in the acknowledgments section we thank Lisa Castlebury for supplying the data from the U.S. National Fungus Collections.

Reviewer #2: There are several phrases in the manuscript (line 139, line 257, line 290-91) which give rise to the idea that modeling analyzes have been done to support these claims. I suppose this has not actually been done, and therefore such claims should be reviewed and softened. On the contrary, all modeling procedures should be reported.

Response: We understand the reviewer concern. So far, no species distribution models have been performed to support this claim. Line 139 has been rewritten to take in consideration the reviewer concern. “Based on occurrence data, we suggest a latitudinal shift among different types of climates where some species are clearly concentrated in some types of ecosystems.” Also, on line 257 “We encourage authors to provide precise coordinates for occurrence data to improve the understanding of Botryosphaeriaceae species distribution.”

Reviewer #2: paragraph 8. Don't forget species substitution by species with better fitness, unless you mean it in point (5), but the concept has to be expanded.

Response: We understand the reviewer concern. However, so far there are no reports on biotic interactions with the capability to actively constrain Botryosphaeriaceae species distribution. And for that reason, we suggest that only when host-specificity is demonstrated, whether for a fungal species with limited ability to colonize and persist endophytically in certain hosts or/and for species with limited ability to infect and express disease symptoms in a certain type of hosts, is assumed that biotic interactions (B) can shape the geographical distribution.

Reviewer #2: paragraph 10. An approximate scheduling of the database update must be provided.

Response: Minor fixes will be updated as soon as possible. A major updated on the source data would be performed every January. The text was changed to reflect the reviewer concern “Major updates on the source information are expected to happen every January and new features may be added over time as a result of users’ feedback.”

Reviewer#2: Data availability, include code.

Response: As mentioned before a GitHub was created and a download function will be available after publication to download the source data as .csv file.

Reviewer#2: About the site, it would be useful to have the direct link to NCBI clicking on accessions.
 For each entry I discovered not all the markers were available; the sentence at line 61 must be clarified.
In my opinion, the climate data tab might be dropped, and data embedded in geographical tab. In fact, it's a bit confusing always having the table above the picture with all the entries, and the user has to search for the species. It would be better if the records from the specific species appear after the selection by user, in Geographical tab.

Response: We thank the suggestion to direct link NCBI accessions. It has been implemented and is already available. Regarding the climate data tab, we change the order of the table to avoid confusion. New tabs might be created in the future depending on User’s feedback.

In line 61 sentence was clarified according to the reviewer’s suggestion “. For each isolate, when available, sequences from the internal transcribed spacer region of the rRNA region (ITS), translation elongation factor 1-alpha (tef1-α), beta-tubulin (tub2), second largest subunit of RNA polymerase II (rpb2) and two alternate forms of the MAT locus (MAT1-1-1 and MAT1-2-1) were selected.”