In the manuscript "Molecular technologies ending with ‘omics’: The driving force toward sustainable plant production and protection", the authors presented a review of the basic concepts of selected omics technologies, with some examples. The authors have reviewed the technologies of four omics applications, including genomics, transcriptomics, metabolomics and metagenomics.
Major points:
The authors cited the technologies applied to omics studies, but the authors did not cite very important literature where the basics of each technology was coined. The explanations are mostly superficial, and no depth is given to any of the omics technologies presented, specially connecting to studies of plant production or protection. The statements do not include any particularity of the cited references, so the information that it presents is basically general information. (E.g. "Proteomics is the study of the total number of proteins expressed in an organism and is divided into several categories, including sequence, structural, functional, and expression proteomics.
51 ).
As a review document, the text should give deep and detailed knowledge about the basic concepts, explore several evidences that drive the topic recently and present an insightful discussion towards the main purpose of the review of exploring omics data generated in studies developed towards sustainable plant production and protection.
For instance, basic statements such as "Important chaperones, such as heat shock proteins, have been identified during proteome functional analyses in wheat and sugarcane.
74 ") should include some more details about the aspects connecting this study to sustainability or plant protection. A discussion on how important this information is should be discussed. This kind of basic structure of citing the information without deep discussion should be avoided and this pattern should be reviewed thoroughly in the text.
It would be important to see not only the citation of omics technologies, and associated tools, but rather which information theses technologies are providing recently that can benefit the sustainable plant production and protection, and how the omics technologies and data generated through theses analysis are providing insightful information that could guide further sustainable applications.
Minor points:
Some citations have no connection with the text (E.G. reference 51, reference 81). It would be important to revise this pattern in the whole text and just cite references directly connected to the information described in the manuscript.
Citations dated over 10 years (E.G. Reference number 40) should be avoided if connecting to recent or current applications (E.G. The development of DNA microarray technology has recently resulted in a significant increase in the sensitivity and throughput of expression screening.
40 ).
The current discussion brings no insights on how the omics technologies can contribute to sustainable plant production and protection
No competing interests were disclosed.
Systems biology, proteomics, biochemistry, molecular biology.
Open Peer Review
https://f1000research.com/articles/12-480/v1#referee-response-260032
Major points:
The authors cited the technologies applied to omics studies, but the authors did not cite very important literature where the basics of each technology was coined. The explanations are mostly superficial, and no depth is given to any of the omics technologies presented, specially connecting to studies of plant production or protection. The statements do not include any particularity of the cited references, so the information that it presents is basically general information. (E.g. "Proteomics is the study of the total number of proteins expressed in an organism and is divided into several categories, including sequence, structural, functional, and expression proteomics.51 ).
As a review document, the text should give deep and detailed knowledge about the basic concepts, explore several evidences that drive the topic recently and present an insightful discussion towards the main purpose of the review of exploring omics data generated in studies developed towards sustainable plant production and protection.
For instance, basic statements such as "Important chaperones, such as heat shock proteins, have been identified during proteome functional analyses in wheat and sugarcane.74 ") should include some more details about the aspects connecting this study to sustainability or plant protection. A discussion on how important this information is should be discussed. This kind of basic structure of citing the information without deep discussion should be avoided and this pattern should be reviewed thoroughly in the text.
It would be important to see not only the citation of omics technologies, and associated tools, but rather which information theses technologies are providing recently that can benefit the sustainable plant production and protection, and how the omics technologies and data generated through theses analysis are providing insightful information that could guide further sustainable applications.
Minor points:
Some citations have no connection with the text (E.G. reference 51, reference 81). It would be important to revise this pattern in the whole text and just cite references directly connected to the information described in the manuscript.
Citations dated over 10 years (E.G. Reference number 40) should be avoided if connecting to recent or current applications (E.G. The development of DNA microarray technology has recently resulted in a significant increase in the sensitivity and throughput of expression screening.40 ).
The current discussion brings no insights on how the omics technologies can contribute to sustainable plant production and protection
Is the topic of the review discussed comprehensively in the context of the current literature?
Partly
Are all factual statements correct and adequately supported by citations?
No
Is the review written in accessible language?
Partly
Are the conclusions drawn appropriate in the context of the current research literature?
No
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Systems biology, proteomics, biochemistry, molecular biology.
https://f1000research.com/articles/12-480/v1#referee-response-260032
https://f1000research.com/articles/12-480/v1#referee-response-201458
Research methodology section is inadequate. Otherwise remove it completely or qualify the number of papers selected, provide a clear criterion for selection and exclusion, including key terms related to plant production and protection used during the selection of papers used, number of records (papers) retrieved using databases as well as other restrictions and relevance criteria. The issues raised above are important and can be improved.
The text under “Limitations of Genomics Technologies” completely failed to cover the subheading/topic, please revise the paragraph.
Figure 1, including other illustrations should be positioned just after being cited for the first time in the text.
Under Transcriptomics (1st paragraph, line 10) specify the kind of analysis serving as a challenge.
Avoid using “…including such as…” in the same line throughout the text.
Any published report/evidence of metabolite profiling in relation to plant protection could have been great.
Lastly, several typos were observed:
Is the topic of the review discussed comprehensively in the context of the current literature?
Yes
Are all factual statements correct and adequately supported by citations?
Yes
Is the review written in accessible language?
Yes
Are the conclusions drawn appropriate in the context of the current research literature?
Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Plant Biotechnolgy
https://f1000research.com/articles/12-480/v1#referee-response-201458