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Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals 2021, 11(7), 2006; https://doi.org/10.3390/ani11072006

by Hongyu Liu^1,2,†, Ibrar Muhammad Khan^1,2,†

, Huiqun Yin³, Xinqi Zhou¹, Muhammad Rizwan¹, Jingyi Zhuang¹ and Yunhai Zhang^1,2,*

Reviewer 1: Anonymous

Reviewer 2: Anonymous

Reviewer 3:

Dominga Soglia

Animals 2021, 11(7), 2006; https://doi.org/10.3390/ani11072006

Submission received: 17 June 2021 / Revised: 28 June 2021 / Accepted: 30 June 2021 / Published: 5 July 2021

(This article belongs to the Special Issue Reproductive Biology of Animals: A Focus on Gamete Biology and Role of Antioxidants)

Round 1

Reviewer 1 Report

All comments were corrected.

Author Response

Riviewer1

1. All comments were corrected.

Response: Thank you very much for the good comments.

Reviewer 2 Report

First of all I want to thank the authors for their efforts in revising the manuscript that in the present version is now more understandable for the readers. In my opinion it is now acceptable for the publication.

Author Response

Reviewer 2

First of all I want to thank the authors for their efforts in revising the manuscript that in the present version is now more understandable for the readers. In my opinion it is now acceptable for the publication.
Response: Thank you very much for the nice comments.

Reviewer 3 Report

Excellent work! The exposure is clear and fluent, the methodological approach comprehensive and thorough, the results are very interesting.

Author Response

Reviewer 3

Excellent work! The exposure is clear and fluent, the methodological approach comprehensive and thorough, the results are very interesting.
Response: Thank you very much for the nice comments.

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

The study fromshows an existence of interactive mRNAs and lncRNAs network which, at the molecular level, is involved in the regulation of spematogenesis in bull testesThe study (manuscript ID: animals-1214294) from Liu et al., shows an existence of interactive mRNAs and lncRNAs network which, at the molecular level, is involved in the regulation of spematogenesis in bull testes. Study is interesting and provides valuable data , it requiresan improvemen in several aspects.

1.Working hypothesis and aim of the study are missing in the manuscript. Research was performed on two selected and age-different groups of animals. In the Introduction paragraph, however, there is no clear explanation concerning the rationale of their experimental choice as well as whether transcriptomic profiles differences between those grousp were expected.

The present version of the Statistical analyses paragraph, suggest (however it is not clearly stated) that also for qPCR results analysis a parametric t-test has been chosen. Such choise raises doubts due to the extremly low abundance of experimental groups (n=3). In fact nonparametric rank-test appears of special usefulness to analyze data on relative mRNA expression levels that were obtained by comparative quantitative method.

3.Discussion paragraph would be improved with more detailed focus concerning differences between two analyzed groups. For example statements like: ‘(…) we identified 6849 lncRNAs significantly upregulated and 2264 were down-regulated between two groups (…) does not inform about association with animals age (how many lnc RNAs and mRNAs were up/down- regulated in each group).

A serious editorial shortcoming of the manuscript is due to its figures illegibility in Acrobat version. In fact, Authors should keep in mind that some potential readers may prefer printed version of the paper to be studied. Therefore, to fulfill a required editorial standard, a comprehensive graphic revision (with special focus on fonts size) of figures is indispensable.
A careful point-to point examination concerning the descriptions given on the figures vs descriptions given in the legends is necessary since some details appear confusing For example on Fig 3 b a given description of the (predominantly) yellow graph is „lncRNA classification”, whereas the legend to Fig 3b there is informs that it refers to „ distribution of circRNAs”. Moreover, why letter „b” was introduced twicely into the legend concerning Figure 3?
Why SEM values are not included on graphs concerning qPCR results obtained on calf group and and why only on some graphs from bulls group the specific SEM value is present (for both see Fig 8)? Whereas when referring to the Figure 8 legend, a reader can find an explanation that „the data are present as the MEAN ± SEM”
It would be advisable to improve the English edition of the manuscript.

Author Response

Dear Reviewer!

Please find the attached file having our point by point response of your kind comments.

Author Response File: Author Response.docx

Reviewer 2 Report

The article describes an extensive Analysis of mRNA and long non-coding RNA Expression Profiling Differences Associated with Testicles Development in Chinese local cattle (Bos taurus). Despite the topic is interesting to those with closely related research interests, there are few issues that need further consideration.

#Minor

Page 14 – “…..suggested that the correlation coefficient should be greater than 0.95.”

Page 15 – In the sentence: “The findings of the GO enrichment study revealed that there were 70 GO description were significantly observed (P-adj-value < 0.05),…” remove the second “were”

Author Response

Dear Reviewer!

Please find the attached file, which containing our point by point response of your kind comments.

Author Response File: Author Response.docx

Reviewer 3 Report

The authors presented a paper on extensive analysis of mRNA and long non-coding RNA expression profiling differences associated with testicle development in Chinese cattle.

The work is well conducted. In my opinion the paper is worthy of publication even if several revisions are requested before to further process the manuscript.

General comment: please include again the number of lines as in the MDPI template file. The absence of line numbers makes the reviewer work so strong. For this reason all my following comments are referring onyl to the page number.

The material and methods section is quite strong to read. I suggest to considerably summarize this section that is really too long.

In the abstract section try to avoid, where possible, the use of acronyms.

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Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

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