Morphological and Phylogenetic Analyses Reveal Four New Species of Gnomoniopsis (Gnomoniaceae, Diaporthales) from China

Round 1

Reviewer 1 Report

Dear Author

I read the manuscript. It is so valuable manuscript with so nice microscopic photographs and multi-locus phylogenetic analyses. There are some minor corrections which highlighted in the text. The main questions are:

1- Gnomoniopsis angolensis, Gnomoniopsis agrimoniae, Gnomoniopsis rosae have also sequence data. However they have not included in the phylogeny. It is recommended to add these species to the phylogeny. 

2- In the mycobank there are 32 species of Gnomoniopsis. However the authors stated that (in the line 271) they accepted 26 of them. Why? in the Key presented for Gnomoniopsis species, why some species such as Gnomoniopsis acerophila, Gnomoniopsis castaneae, Gnomoniopsis cincta, Gnomoniopsis nicotianae, Gnomoniopsis piperata, Gnomoniopsis vanillae are not included. Please add these species to the key as well.

3- Please add the Fasta file of alignments as supplementary material.

All the best

Comments for author File: Comments.pdf

Author Response

1.    including 
I accepted the suggestions.

2.    Here you can add a few sentence about the number of the Gnomoniopsis species and how many of them have sequence data?
I accepted the suggestions.

3.    Pleas check are these culture collections registered internationally? If not, Please also deposit the type material to a registered culture collection such as CBS or etc.
Yes. The “HSAUP” is a temporary herbarium for us to deposit our voucher specimens in Shandong Agricultural University. After our research is completed, we will send the voucher specimens to the Mycological Herbarium of Microbiology Institute, Chinese Academy of Sciences, Beijing, China (HMAS).

4.    Gnomoniopsis angolensis 
Gnomoniopsis agrimoniae
Gnomoniopsis rosae 
have also sequence data. So please add these species to the phylogeny.
Although they have sequence data, most sequences are missing (G. angolensis and G. rosae only ITS sequence can be used, and G. agrimoniae only “UNVERIFIED” tef1 sequence). I have tried to build ML tree, the effect is very poor, I have sent it to the supplementary material, please refer to it.

5.    Please put the BIPP and MLBV values on the branches.
I accepted the suggestions.

6.    : MB
I accepted the suggestions.

7.    Should not be in format? XX° XX′ XXʺ N
I accepted the suggestions.

8.    it is better to say loci. 
ITS is not gene.
I accepted the suggestions.

9.    What is this? Pleas check!
I accepted the suggestions and revised it.

10.    In mycobank there are 32 species of Gnomoniopsis. Please clarify what do you mean here "we currently accepted"! For example, why the following species are not included in the Key?
Gnomoniopsis acerophila
Gnomoniopsis castaneae
Gnomoniopsis cincta
Gnomoniopsis nicotianae
Gnomoniopsis piperata
Gnomoniopsis vanillae
I think some fungi are not recognized because of the difficulty of morphological description and the existence of synonyms. So I mainly refer to Walker’s two literatures for this key, and try my best to find the morphological characteristics of each species.
G. castaneae should be considered as a synonym of G. smithogilvyi.

Reviewer 2 Report

Wang et al propose the introduction of four novel species of Gnomoniopsis. Their data seems to support it.

However, I have some suggestions to improve the manuscript before it can be accepted.

Line 14: (ITS) region the ribosomal RNA gene cluster. (ribosomal DNA does not exist. Ribosomes do not have DNA).

Line 14-15: and partial regions of the genes ….

Lines 44-49: here I miss a clear description of the goal of this study. Authors jump from “fungi were collected” to “species descriptions”. Clearly define the goal.

Line 63: Micromorphological characters directly from specimens collected or from structures produced in culture by the fungi? It is not clear.

Line 69-73: I would like to see the ex-holotype cultures deposited in an internationally recognized culture collection where it can be easily accessed. This is of primary importance for taxonomic studies. Also, storing ex-type cultures in more than on culture collection is safer in case some problem occurs with one of them.

Line 96: not sure what it means being used as backbones.

Line 99-100: did the authors check for incongruencies between individual phylogenies. Explain how?

Line 115: results start immediately with phylogenetic analyses. I miss a section here describing how many plants samples were collected and analyzed.  How many fungal isolates were obtained and how did you reach the conclusion that all belonged to Gnomoniopsis. 

Line 238: something does not belong here!

Line 334: the discussion is rather short. Maybe the authors can expand a little bit.

Line 359: was illustrated. Also, you mention 13 countries, but Michigan is not a country. It is part of the USA. 

Line 362: you could also cite this study (https://link.springer.com/article/10.1007/s10658-016-0912-z) which describes the occurrence of Gnomoniopsis smithogilvyi on hazelnut in Italy.

Author Response

1.    Line 14: (ITS) region the ribosomal RNA gene cluster. (ribosomal DNA does not exist. Ribosomes do not have DNA).
I accepted the suggestions and revised it.

2.    Line 14-15: and partial regions of the genes ….
I accepted the suggestions.

3.    I Lines 44-49: here I miss a clear description of the goal of this study. Authors jump from “fungi were collected” to “species descriptions”. Clearly define the goal.
I accepted the suggestions.

4.    Micromorphological characters directly from specimens collected or from structures produced in culture by the fungi? It is not clear.
I accepted the suggestions.

5.    Line 69-73: I would like to see the ex-holotype cultures deposited in an internationally recognized culture collection where it can be easily accessed. This is of primary importance for taxonomic studies. Also, storing ex-type cultures in more than on culture collection is safer in case some problem occurs with one of them.
I accepted the suggestions. The “HSAUP” is a temporary herbarium for us to deposit our voucher specimens in Shandong Agricultural University. After our research is completed, we will send the voucher specimens to the Mycological Herbarium of Microbiology Institute, Chinese Academy of Sciences, Beijing, China (HMAS).

6.    Line 96: not sure what it means being used as backbones.
Make the main reference.

7.    Line 99-100: did the authors check for incongruencies between individual phylogenies. Explain how?
Due to the small sequence gap of a single gene, the individual evolutionary analysis is slightly different, but the effect is not large, and the multi-locus analysis is more reliable.

8.    Line 115: results start immediately with phylogenetic analyses. I miss a section here describing how many plants samples were collected and analyzed.  How many fungal isolates were obtained and how did you reach the conclusion that all belonged to Gnomoniopsis.
I did not count how many strains were isolated from one specimen, but the number would not exceed 10, and not all fungi isolated from one specimen belonged to Gnomoniopsis. In the process of separation and purification, roughly distinguish what group it is by observing the characteristics of the colony, and then put them together for analysis.

9.    Line 238: something does not belong here!
I accepted the suggestions and revised it.

10.    Line 334: the discussion is rather short. Maybe the authors can expand a little bit.
I accepted the suggestions and revised it.

11.    Line 359: was illustrated. Also, you mention 13 countries, but Michigan is not a country. It is part of the USA. 
I accepted the suggestions and revised it.

12.    Line 362: you could also cite this study (https://link.springer.com/article/10.1007/s10658-016-0912-z) which describes the occurrence of Gnomoniopsis smithogilvyi on hazelnut in Italy.
I accepted the suggestions and add it.