PONE-D-21-40096Characterization of Colletotrichum alatae causing yam anthracnose in Cross River State, NigeriaPLOS ONE

Dear Dr. Otang

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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ACADEMIC EDITOR: Reviewers raised several valid questions in the manuscript and provided useful comments. Therefore, I suggest to the authors follow the reviewer's comments to modify the manuscript. Recommended for major revision.

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Additional Editor Comments:

Reviewers raised several valid questions in the manuscript and provided useful comments. Therefore, I suggest to the authors follow the reviewer's comments to modify the manuscript. Recommended for major revision.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: No

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear Author

Your submission entitled "Characterization of Colletotrichum alatae causing yam anthracnose in Cross River State, Nigeria" has been reviewed.

Kindly resubmit the manuscript with corrections in track changes mode, the other one, with clear manuscript).

Regards,

Reviewer #2: Comments

The manuscript entitled “Characterization of Colletotrichum alatae causing yam anthracnose in Cross River State, Nigeria” deals with the characterization of the Yam anthracnose pathogen through morphological, cultural, and molecular methods. Eight isolates of Colletotrichum spp. was obtained and sequence analysis revealed that the isolates are distinct. Screening the landraces with the virulent isolate, showed differential reaction which will help in breeding yam for anthracnose resistance. The paper provides information about the Yam pathogen in Cross river State, Nigeria, which is important to understand the etiology of the pathogen and the spread of the disease within the community. The diversity of C. alatae is said to result from its high potential for gene flow; and its virulence, might be due to recombination of its virulence alleles. However, some data should be appended and re-oriented to improve the quality of the paper. Overall, the English language can be improved and there are some grammatical errors which need to be corrected.

Abstract:

The abstract is written well. However, some of the data are misleading in screening the landraces which are repeated esp . … 15.15% were moderately resistant (MS), which is wrongly represented. 18.18% were resistant while 18.18% were highly resistant (HR). The data is not clear.

Introduction:

Can be shortened and the importance of Yam can be reduced. Instead the authors can focus in the disease and the present control measures followed. Besides, the international status of the disease and pathogen can also be represented as described by other scientists.

Materials and Methods:

Should be clear and concise and the methodology should be described. The cultural and morphological characters used for identification were not mentioned in this section. The type and methods of survey carried out can be elaborated. While using a scale, you can follow percent disease index rather than incidence. Any previous reference is there for disease scale. Why data were recorded 16 weeks post inoculation? Whether the symptoms appeared only by that time? How long the plants were maintained in the glass house. In soil or in pot culture?. The concentration (spores/ml) of the inoculam should be mentioned. Statistical analysis followed should be included. How many replications were made for the screening experiment. How many plants were used for landraces/accessions for screening?

Results

The result section can be reduced and at present it is elaborate. Some queries which are observed in the result are

i) The figures and tables can be reduced. Some tables can be deleted viz., Table 5 and Table 6. Table 3 can be given as a supplementary file. Similarly, Table 7 & 8 can be clubbed and the disease incidence and reaction can alone be presented as a single table.

ii) Whether rapid growth in plate is directly proportional to the virulence can be explained.

iii) Whether any specific difference in mycelial growth pattern was observed. Whether Acervuli was observed in the isolate in the diseased specimens. You can document the data to see the difference. Any sexual fruiting body was observed in the cultures viz., Perithecia. Since it deals with differentiating Colletotrichum spp. these characters are important. No conidial photos of the isolates were presented. Is there any variation of the hyaline, single celled conidia of C. alatae with respect to C. gloeosporioides observed as there exist variation among the species of Colletotrichum.

iv) Amplification of ITS region cannot differentiate within species level. If there are any SCAR markers specific for C. gloeosporioides, it can be used to differentiate C. alatae.

v) Some RAPD and ISSR primers can be used to differentiate the isolates which can be used to identify the marker unique in C. alatae .

vi) The accession number to the sequenced isolate can be given instead of the sequence.

vii) The variation in the sequence with respect to C. gloeosporioides can be highlighted if the authors justify the portion of the genome which is variable.

viii) The sequence of CA11 presented in Table 5 if blasted in NCBI database does not any match to C. alatae. Rather it shows identity to Lasiodiplodia theobromae. Justify.

ix). Whether you have submitted the sequence in the NCBI or any other database and the accession number obtained is not clear.

x). Disease incidence of 41-60 % is given as moderately resistance which looks very high. If the plant is 60 % infected how can we place in the resistant category. Pl. refer the reference for the reaction scale.

Discussion

It can be reduced to a certain extent and the main point alone can be discussed. However, the authors have substantially discussed the variation within the pathogen that may have arised due to recombination/gene flow.

Conclusion :

Conclusion should directly depict the results from the manuscript and its application in future can be highlighted.

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Reviewer #1: Yes: Nasir Ahmed Rajput Assistant Professor, Department of Plant Pathology, University of Agriculture, Faisalabad Pakistan

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-21-40096_reviewed.doc

PONE-D-21-40096R1Characterization of Colletotrichum alatae causing yam anthracnose in Cross River State, NigeriaPLOS ONE

Dear Dr. Ntui,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================

ACADEMIC EDITOR: Reviewers raised several valid questions in the manuscript and provided useful comments. Therefore, I suggest to the authors follow the reviewer's comments to modify the manuscript. Recommended for minor revision.

==============================

Please submit your revised manuscript by May 06 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Karthikeyan Adhimoolam

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: N/A

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: The authors have carried out all the corrections as suggested by the reviewer. Now the quality of the paper is improved. But there are many basic flaws which need to be addressed besides some minor corrections.

Minor corrections

Abstract : Spelling mistakes . Need to be carefully addressed throughout the manuscript. Lsidioplodia theobromae, (Lasiodiplodia theobromae).

In the third line include…In the present study, the pathogen…….

End of Introduction Proffer ….

The identity of the isolates in sequencing seems to be very less and should be clarified. Bec. < 75 % identity could not exist within a species. In that case, it should be a different genus.

None of the C. alatae isolates was in the same cluster with the reference sequence indicating that the isolates are distinct……Is not clear, If so how you claim it is C. alatae if it is distinct….Can be rewritten or reframed.

Major corrections

In the materials and methods in whole plant bioassay it is denotes as

Screening of yam for tolerance to C. alatae: Whole plant bioassay

In the above title, you have mentioned tolerance to C. alatae. But challenged with Lasiosiplodia theobromae ……The yam plants were challenged with isolate Lt1 which was the most virulent according to the pathogenicity test. ……….Then the entire experiment goes wrong as it is with a different pathogen. Even though it is highly pathogenic, it is a different pathogen with different spore characters. In that case, the paper should address the importance of two pathogens and not only C. alatae. Bec. The title deals with C. alatae. But the landraces/accessions are screened for L. bromae. The authors will be confused with these statements. Substantiate.

If Lt1 is used for screening the isolates how will you claim it is resistant to Colletotrichum spp? In that case, even the scale used should have a reference as it is general or specific for Colletotrichum pathogens.

In the table 4 in the legends it is still indicated that 41- 60 % is moderately resistant but in response to reviewers it is claimed that > 40 % is considered as susceptible. Clarify.

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Reviewer #1: Yes: Dr. Nasir Ahmed Rajput, Department of Plant Pathology, University of Agriculture, Faisalabad Pakistan

Reviewer #2: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

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Characterization of some fungal pathogens causing anthracnose disease on yam in Cross River State, Nigeria

PONE-D-21-40096R2

Dear Dr. Valentine,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Karthikeyan Adhimoolam

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: N/A

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: No

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: (No Response)

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Reviewer #3: No

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