PONE-D-21-00157

Genome-wide identification, phylogenetic and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L

PLOS ONE

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Farrukh Azeem

Academic Editor

PLOS ONE

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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: The authors reported the identification of 21 LIM genes in alfalfa (Medicago sativa L). They examined the genome distribution, protein physicochemical properties, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the MSLIM family by using extensive bioinformatic tools. These analyses generally worked well. However, I have some points that need to be addressed. They need to work on these aspects before this manuscript is accepted.

1)The members of the family are classified according to the classification standards of Arabidopsis and other model plants, Please write down the names of other model plants.

2)The authors used 10 species to study the evolutionary relationship. LIM family members of 9 species except for Arabidopsis, please provide references or websites.

3) It is suggested that subcellular localization should be predicted using multiple websites.

4)The authors did not state the sampled tissue. Furthermore, it is suggested that the expression levels of 21 LIM genes be detected in different tissues.

5) Some formats and grammatical errors need to be modified.

Reviewer #2: Title: Italicize Medicago sativa

Abstract

use MsLIM01-MsLIM21.

“Using bioinformatics methods,”- bad grammar

Write: “physicochemical properties of protein”

Why only salt and low temperature stresses were explored? Include moisture stress, heat and phytohormone treatments in the experiment.

Introduction

First para of introduction: Italicize all scientific names

Third para: include reference in favour of the statement.

Materials and methods

Arabidopsist haliana L??

Italicize all scientific names

“Use Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) tool to perform multiple sequence alignment of LIM amino acid sequence.” –example of bad grammar.

Section 1.7: Why relative humidity was that low (40%)? Is there any reference in support? What was the light intensity?

What sample was collected? What was control and what was mock?

How many biological replicates?

Section 1.8 what was the source of independent RNA sample? How many technical replicates?

Discuss statistical procedure in methodology.

Results

“Using the Arabidopsis LIM protein sequence and the alfalfa genome sequence to perform BLAST

comparison to extract the CDS and protein sequence of the alfalfa LIM gene, after de-redundancy

and SMART identification, 21 alfalfa LIM genes were finally identified and named as MSLIM01-

MSLIM21.”- bad grammar, data not cited in favour of the statement.

Expression results: No data was tagged.

Discussion

4 Discussion: capitalize D

Data were not tagged properly

“Conclusion - we have a preliminary understanding of the response of this gene in alfalfa after adversity stress, which lays a foundation for its functional verification and will be useful for future cultivation of alfalfa. New varieties of alfalfa and the development of alfalfa industry in northern my country are of great significance.” –rewrite these sentences.

Tables and Figures

What is SRS in Table 1.

Figure 1: Italicize all scientific names. Soybeans or soybean?

Figure 2. Chromosomal location of LIM family genes. Write MSLIM as MsLIM.

Figure 3. Write MSLIM as MsLIM.

Quality of Figure 4 is very poor. Write MSLIM as MsLIM.

Figure 5: what are ‘these orthologs’?

Figure 7: Italicize Medicago sativa. Some genes were highly expressed under low temperature but some others were highly expressed under NaCl treatment. Prepare separate figures for two different treatments. NaCl, not Nacl.

Professional editing is required.

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Reviewer #1: Yes: Lifeng Liu

Reviewer #2: No

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Genome-wide identification, phylogenetic and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L

PONE-D-21-00157R1

Dear Dr. nian ,

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.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Farrukh Azeem

Academic Editor

PLOS ONE

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: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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: Yes

**********

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

**********

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: Italicize botanical names in the reference section and revise references carefully. Carefully edit the manuscript for spacing and other typos.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Arif Hasan Khan Robin