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Dear Authors,
I am pleased to inform you that the manuscript has improved after the last revision and can be accepted for publication.
Congratulations on accepting your manuscript, and thank you for your interest in submitting your work to PeerJ.
With Thanks
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
All the issues have been addressed, no further comments.
All the issues have been addressed, no further comments.
All the issues have been addressed, no further comments.
Dear Authors
The manuscript still needs a minor revision. The authors are invited to revise the paper considering all the suggestions made by the reviewer. Please note that the requested changes are required for publication.
With Thanks
Line 1: remove “g” from the word “Identification”.
Line 43: “subsp.” should not be italicized.
Line 50: replace “namely” with another word that matches the context.
Separate the word from the parenthesis. This happens in lines 48, 55, 58, 60, 64, 66, 67, 68, 75, 76, 80, 87, 94, 180, 182, 311, 312, 314, 316, and 387.
Arabidopsis thaliana needs to be italicized in lines 146, 254, 255, and 262.
Line 181: substitute “by” with “with”.
Line 200: replace “suspension” with “solution”.
Line 203: Agrobacterium tumefaciens needs to be italicized.
Line 214: replace “so on” with a more academic phrase.
Line 217: The authors state that “the ranges make the study … more difficult”. Please further develop this idea.
Line 276: Replace the dot with a proper punctuation.
Line 276 and 277 are short sentences, please rephrase and include them in one sentence.
Line 335: correct citation.
No comment
Line 80: The author argues that while enhancing the host plant's resistance is considered the most effective strategy, it is widely acknowledged that pests eventually develop ways to overcome this resistance. This apparent contradiction highlights the current issue at hand. Therefore, the aim of this paper is to address this challenge and propose innovative solutions, please rephrase to show the idea accordingly.
Figure 5: it’s difficult to visualize, please include a figure with a clear definition.
Dear Authors
In your response to the reviewer, the authors mentioned that Arabidopsis RRM1 genes have been preliminarily identified. This provides an essential reference for researching rice's RRM1 gene family and gene function. Accordingly, it is fundamental to reconstruct the Phylogenetic tree and include the RRM1 Arabidopsis genes to cluster the rice genes according to Arabidopsis genes. In addition, putting the bootstrap value for every clade/group is essential.
Furthermore, the authors enriched all RRM1 genes by GO and KEGG, focusing on the genes enriched in biological stress and immune response. However, it is vital to provide evidence or cite a reference confirming the selected genes' roles in the immune response.
It is also suggested to do domain analysis and determine where the difference is for every RRM1 gene group, characterize every clade by domain, and highlight the difference between every clade; at that point, the authors can select one gene from each group to validate their role in the immune response using qPCR.
**PeerJ Staff Note:** Please ensure that all review and editorial comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the response letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the response letter. Directions on how to prepare a response letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/.
Best Regards
Comments are not addressed properly
Not well designed. Asked to address during revision, but have not addressed them.
I asked for RNA experiment validation for genes from each phylogenetic group. However, authors failed to do that.
I suggest to reject this MS
Authors has taken an important topic of biotic stress management in rice. The out come of the work may be useful for the management of blast disease in rice.
The experimental design is sound. the investigation of OsRRM1 gene family may help for the creation of new resistance line of rice
The figures are fine
Authors has attempted to investigate the OsRRM1 gene family for the cambating of Blast pathogen control.
Dear Corresponding Author,
I am writing to inform you that we have received the reviewers' comments on your manuscript.
The reviewers have provided valuable feedback and suggestions to enhance your research's clarity, quality, and impact. Please carefully review the reviewers' comments and suggestions and revise your manuscript accordingly.
Furthermore, improve the resolution of all the figures! Each figure or table should be self-explanatory! Use clear descriptions in the figure, title, or legend.
Please address each comment raised by the reviewers in a detailed response letter explaining the changes made.
Please carefully proofread your revised manuscript to eliminate errors or inconsistencies before submission.
Best wishes,
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
**Language Note:** The Academic Editor has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
Abstract must be clear and explain the whole story in a proper way. I lost while reading the abstract. For instance, authors discussed about gene expression at L24-29 and again at L37-42. I suggest to make a significant improvement in the abstract.
All genes and species names must follow the standard IUPAC format: L83 “OsRRM1” must be italic; L77 “Oryza sativa Japonica” must be “Oryza sativa subsp. japonica”; L85 “Magnaporthe Oryza” must be “Magnaporthe oryza”; L 117 No need to use full genera name every time; 169 The experimental material is rice (O.Sativa L.spp.japonica,var nippobare); L178 “Magnaporthe Oryza”; L211 “Agrobacterium tumefaciens”; L217 “(Oryza sativa Japonica)”; L236 “OsRRM1” etc.
I lost while reading material and methods, which needs to be improved.
L169-174 I suggest authors to explain this section properly. Specially, I am wondered how PCR plates were used to grow the seedlings? If this is possible, I suggest to include some pictures as supplementary figure.
Why authors used “nippobare” line
Why expression analysis is described at two places. One at L157-168 and other at L175-195. RNA seq experiment need to be explained properly. Weather RNAseq was done at seedling (L175-195) and adult plant stage (L157-168), if this is yes, why authors did at different time points? There is much confusion in this section, needs to be clear.
Authors mentioned Insilco subcellular localization of RRM1 in L126-128. However, they explained the invitro protocol in L195-212. Why do authors make this much confusion in this section?
L154 why do authors selected 2000bp upstream of gene was use to predict the promotors.
L270-275 if this is the case, what about remaining 192 genes from rice? Do authors think, all of them were originated after diversion monocots from dicots (i.e., Arabidopsis)? Additionally, I suggest to include phylogenetic and synteny analysis with other cereals such as maize and wheat.
L305-310 what is the basis of selecting four genes for qRT-PCR analysis? Mention the gene names in text. Again, I suggest to include the at least one gene from each group (based on five phylogenetic groups). So that you can see the difference in the expression of genes over different groups also.
L312-318 why do authors selected OsRRM1-15 and OsRRM1-207 for subcellular localization study?
I suggest to include botanical name of rice in title
There are no keywords in the MS
Content wise introduction is good. However, writing is very poor. So, I suggest to improve the grammar by contacting professional writers. Some of them includes:
Sentence need to reframed
• L85-86 “Magnaporthe Oryza is one of the most widespread and harmful worldwide fungal diseases caused by rice blast fungus”
• L91-93 “The resistance of germplasm resources has a wide range of genetic variation, and thus the host plant's own resistance is the most effective, economical and environmentally friendly method to against Magnaporthe Oryza(Manandhar et al. 1998)”
L170 Use abbreviation of NaClO
What is “et al.” in L222 and L283
L226-228 I suggest to include some figure for this information.
I suggest to move Table. 2 as supplementary table.
Figures quality is too poor. Needs to improve the figures.
I suggest authors to mention group names in Fig 3 and Fig 4
L263-269 I suggest to include the figure for this section as a main figure and move Figure 4 as supplementary
L287-292 “TGACG motif (involved in JA response)” mentioned twice
1. Paper entitled " Identification of Rice RRM1 Gene Family and Its
2 Functional Study in Rice Blast: comes under the scope of Journal.
2. Sufficient field background/ context provided.
3,.In the abstract, add one or two sentences about the challenges of the study and later discuss the contributions made.
The experimental design is OK. I would suggest authors add the pictures of Rice treatment with M.oryzae if they have one.
Authors are requested to improve the grammar, spelling, and presentations. The paper needs careful English polishing since there are many typos in written sentences and scientific names of the crops/pathogens.
Authors are advised to add the future scope of the study, in the conclusion.
4. Overall the manuscript deserves for publication after the revision and corrections indicated in the manuscript.
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