Diversity of Unusual Ribosomal Genes and Ecological Origin of Rice (Oryza spp.)

Round 1

Reviewer 1 Report

Xiyu Tan et al. submitted their study about “Diversity of unusual ribosomal genes and ecological origin of rice”. Authors obtained unusual ribosomal gene sequences from Oryza species that showed great diversity. The diversity of rDNA sequences indicated that the homogenization in rice is incomplete and explains the introgression of distinct rRNA gene families into ancestral rice genome before speciation and continent separation.

Major points

1. Introduction: the purpose of work and importance of study should be clearly reflected in the introduction section.

2. Line 106-114: The content from line 106 to 114 is not relevant to study. Delete it.

3. Materials and methods:  Plant material, and DNA & RNA extraction should not be written under one heading.

4. Conclusion should be clear and understandable to the scientist outside your specific research field.

Comments for author File: Comments.pdf

the minor English editing is required.

Author Response

Thank you so much for the valuable suggestions on the MS. 

Author Response File: Author Response.pdf

Reviewer 2 Report

The manuscript ia an interesting research revealing the diversity in ribosomal genes in rice and its origin, it is well written and presented clearly, however some modifications need to be taken into consideration to imrove the manuscript:

Title

Line 3: add scientific name of rice

Introduction section:

Lines 38-39:

“Genera of the Gramineae, Oryza, does not only provide food for half of the world's population but is also used as a model plant by the scientific community” Should be deleted.

Line 39: “The genus Oryza” you should add “of the Gramineae Genera”Lines 106-114: ??? to be deleted

Material and methods section:

Line 116: Add subtitle “Plant material” where you put a table with the different name of accessions you used with their common name and accession number (that you have mentioned in RNA and DNA extraction) and also their genomic type. To be clear for readers !!!

Besides you should add the provenance of the accessions you used (stored in gene bank or collected or what exactly: you have to specify!!).

If you have picture of these accessions you can add.

In line 123 you have mentioned that these accessions were selected: You should specify the basis of this selection what characteristics these accessions had to be selected, any specific trait?....etc

In The subtitle “RNA and DNA extraction” section you should add more detail of this extraction; such leaves or roots how many grams you used and which age (plants with 2 leaves or haw many days post sowing …etc) and describe briefly how you did your extraction (CTAB method or what ??)

You have to clarify that the extaction and for gene expression; was done from 2 types of plants (those fertilized and those unfertilized) because it is not clear as presented!!!

Line 128: put latin names in italic and verify in the hole document

Results section:

Lines222-224: “Homologs of 98% of the sequenced maize, wheat, and barley proteins are found in rice [29] providing the base for the development of cereals” should be in discussion !

Discussion section

Line 417: “Chang” add refrence number !!!

Conclusion section:

Lines 440-446: (i) to (iii) Should be better in discussion section. Incorporate a sentence highlighting the potential for future research and development by introducing a follow-up study as a valuable perspective.

Reference section:

Verify ref#12

Ref #38 (issue number and pagination is missing !!)

Author Response

Thank you so much for your valuable suggestions and comments. 

Author Response File: Author Response.pdf

Reviewer 3 Report

In this study, the functional characterization of unusual ribosomal gene sequences from Oryza species that showed great diversity, which were absent in the present genomic sequence, was performed. The study also estimated the divergence between the rRNA families in rice. Moreover, the study also showed that the large subunits of ribosomal genes of all families are expressed depending on N fertilization of the plants. Generally, the study is of interest and a good level of effort was performed.

In my opinion, the paper needs to be improved across different sections, as has been shown directly in the manuscript (attached). The main points are:

·       The introduction section needs to be checked carefully and clarify the highlighted words, sentences, or phrases. Please delete the template guides at the end of the section.

·      I think it could be better to convert some parts in the Materials and Methods to a table. Please also check the highlighted parts. I think you need to give more details on growing the plants for more clarity.  

·      I have the feeling that there is some kind of a mix-up between the results and the discussion in this paper. Therefore, the flow of results is not smooth and it is not easy to follow.

·      I think the conclusions do not emphasize the main finding of the study, i.e. the unusual ribosomal gene sequences from Oryza species, which showed great diversity and did not appear in the present rice genome sequence. May I suggest that you try to summarize or chart your most important findings because extracting them from such large figures is not easy.

·      Different citation styles were sometimes used, which led to missing their inclusion in the reference list.

Additional editings are provided in the attached file.

Comments for author File: Comments.pdf

Generally, the English language is good but some editing is needed for more larity.

Author Response

Thank you so much for your valuable suggestions and comments.

Author Response File: Author Response.pdf