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Peer-Review Record

Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill

Plants 2019, 8(4), 87; https://doi.org/10.3390/plants8040087

by Zerui Yang^1,†

, Yuying Huang^1,†

, Wenli An¹, Xiasheng Zheng¹

, Song Huang^1,* and Lingling Liang^2,*

Reviewer 1: Anonymous

Reviewer 2: Anonymous

Reviewer 3: Anonymous

Plants 2019, 8(4), 87; https://doi.org/10.3390/plants8040087

Submission received: 21 February 2019 / Revised: 29 March 2019 / Accepted: 31 March 2019 / Published: 3 April 2019

(This article belongs to the Special Issue Plant Bioinformatics)

Round 1

Reviewer 1 Report

Yang et al. have sequenced the chloroplast genome of an important chinese herb Lycium chinense Mill. This study presents comprehensive analyses of the chloroplast genome sequence and might be of interest in the herbal medicine community.

However, the authors' claim that this is the first chloroplast genome sequence in the Lycium genus is erroneous. Lycium barabarum and Lycium ruthenicum chloroplast genomes have been published in 2018. Therefore, authors need to include this information in their introduction, include these species in their comparative analyses + phylogenetic tree in the results and discuss the resulting implications in discussions and conclusions.

The other major concern is that the abstract and contents of the manuscript are riddled with grammatical errors and in some places, even spelling errors. The authors need to engage a professional to go over and correct the language and grammar of the paper.

Minor comments:

Line 220-221: the authors need to to mention which filtering/trimming tool was used to clean the short reads and also cite the relevant paper.

Line 30: What is meant by 'functional food'? The citation [2] does not seem to be correct.

Overall, I would like the authors to resubmit for review after the major concerns are addressed. Then, the reviewers will be able to provide a more detailed feedback.

Author Response

Dear reviewer:

Thank you so much for your advice. I have revised the article according to your advices.

Point 1: However, the authors' claim that this is the first chloroplast genome sequence in the Lycium genus is erroneous. Lycium barabarum and Lycium barabarum chloroplast genomes have been published in 2018. Therefore, authors need to include this information in their introduction, include these species in their comparative analyses + phylogenetic tree in the results and discuss the resulting implications in discussions and conclusions.

Response 1: Thank you so much for your advice. I am so sorry for this, I haven't found any articles about the chloroplast genome of these two species, Lycium barabarum and Lycium ruthenicum chloroplast genomes. And according to your advice，I have included this information in our introduction, include these species in our comparative analyses and phylogenetic tree in the results and discuss the resulting implications in discussions and conclusions.

Point 2: The other major concern is that the abstract and contents of the manuscript are riddled with grammatical errors and in some places, even spelling errors. The authors need to engage a professional to go over and correct the language and grammar of the paper.

Response 2: Thank you so much for your advice. I am so sorry for this, And according to your advice，I have engage a professional to go over and correct the language and grammar of the paper.

Point 3: Line 220-221: the authors need to to mention which filtering/trimming tool was used to clean the short reads and also cite the relevant paper.

Response 3: Thank you so much for your advice. And according to your advice，I have mentioned which filtering/trimming tool was used to clean the short reads and also cite the relevant paper.

Point 4: Line 30: What is meant by 'functional food'? The citation [2] does not seem to be correct.

Response 4: Thank you so much for your advice. And according to your advice, I have corrected the citation [2]. And I think functional food refers to a food with a specific function, suitable for a specific group of people to eat, can adjust the function of the body, and not for the purpose of treatment. I have deleted this words from the manuscript, since It will produce ambiguity.

Reviewer 2 Report

In this study, the authors sequenced and assembled the chloroplast genome of Lycium chinense. As such it is yet another study where a chloroplast genome is exhaustively reported. It may potentially be published in Plants – eventually. At the moment, the main problem is language. This starts with typos and ends with wacky sentences. The authors need to use a language service or have a native English speaker revising the manuscript before it can be thoroughly evaluated.

From a technical view, most analyses are fine. Tables S1-S3 should be removed from the actual manuscript and Table 3 can be deleted. The main problem I see is the phylogenetic analysis, which is very shallow – ideally the authors perform a more thorough analysis where they estimate divergence times, e.g. using BEAST. Also, the best phylogenetic model should be estimated using the program ModelTest. Note that you report only 100 bootstraps in the figure and 1’000 in the methods.

Another major issue I see are the references, which seem to be randomly picked – lick citations 9 or 10 on page 2. Also, very few citations are used again in the discussion. Please provide a better review of the literature, focusing more on the general processes rather than citing many examples of “here they sequenced another CP genome”. The format of the references is not consistent across all of them.

Lastly, check the manuscript for inconsistencies in numbers – e.g. reporting 130 genes (line 80) and 114 (line 17).

Author Response

Dear reviewer:

Thank you so much for your advice. I have revised the article according to your advices.

Point 1: In this study, the authors sequenced and assembled the chloroplast genome of Lycium chinense. As such it is yet another study where a chloroplast genome is exhaustively reported. It may potentially be published in Plants – eventually. At the moment, the main problem is language. This starts with typos and ends with wacky sentences. The authors need to use a language service or have a native English speaker revising the manuscript before it can be thoroughly evaluated.

Response 1：Thank you so much for your advice. I am so sorry for this, And according to your advice，I have engage a professional to go over and correct the language and grammar of the paper.

Point 2: From a technical view, most analyses are fine. Tables S1-S3 should be removed from the actual manuscript and Table 3 can be deleted. The main problem I see is the phylogenetic analysis, which is very shallow – ideally the authors perform a more thorough analysis where they estimate divergence times, e.g. using BEAST. Also, the best phylogenetic model should be estimated using the program ModelTest. Note that you report only 100 bootstraps in the figure and 1’000 in the methods.

Response 2：Thank you so much for your advice. And according to your advice，I have studied the BEAST software, but I am sorry that I have not fully understood this software yet. I can only add the phylogenetic tree generated by this software into the article (Figure 7), which is exactly the same as the phylogenetic tree generated by the MEGA software(Figure 6). I hope you can forgive me for this. Tables S1-S3 are deleted, and I don't delete the Table 3, because I think it necessary the analyse it , please forgive me about this. And The 100 in the figure means 100%. And I have used the best model to do the phylogenetic analysis.

Point 3:Another major issue I see are the references, which seem to be randomly picked – lick citations 9 or 10 on page 2. Also, very few citations are used again in the discussion. Please provide a better review of the literature, focusing more on the general processes rather than citing many examples of “here they sequenced another CP genome”. The format of the references is not consistent across all of them.

Response 3：Thank you so much for your advice. I am so sorry for this, And according to your advice，I have corrected the fomat of the references，check the references, and the discussion has been revised and add some references to the discussion.

Point 4: Lastly, check the manuscript for inconsistencies in numbers – e.g. reporting 130 genes (line 80) and 114 (line 17).

Response 4：Thank you so much for your advice. But the number is right. 114 plus 16 equals 130.

Reviewer 3 Report

In this paper the authors announce the plastome sequence forLycium chinense, a species endemic to China that produces an edible fruit and is important in traditional Chinese herbology. The science and the methodology seem to be OK but the paper is not ready for publication. Numerous grammatical, sentence construction, and word choice errors occur throughout the paper. The authors should consider having a professor of English or a native English speaker review the text before they resubmit. In my comments below, I have provided some changes regarding how the information is presented but also some English language usage edits. This is not a complete list of edits, as it is out of the purview of a scientific reviewer to highly edit a paper for language usage to the degree that would be required to make this paper acceptable.

Major Changes

Introduction:

Line 28 – “at the magnificent” – the scientific primary literature shouldn’t include hyperbole in its descriptions of cultural traditions. I recommend, “Lycium chinense plays an important role in Chinese traditional medicine.”

What makes this a “functional food”?

Line 36 – “among which Lycium is one of the most important.” What makes this genus “important”?

Lines 42-43 – These sentences contradict one another. The authors site a study where barcodes were effectively used to identify relationships in Lyciumbut then say they are not effective. Which is it?

Section 2.2

Beginning on line 97 there is a comparison of L. chinenseto other species. These other species and their relationship toL. chinensehas not been introduced or described making it difficult for the reader to understand its importance.

Line 99 – what is meant by “forward and palindromic”

Section 2.5

The first paragraph, lines 146-154 is difficult to understand. The second sentence is non-sensical. I can’t tell if the difficulty I’m having is from the author’s English language usage or an incomplete description of the data. It should be rewritten.

Section 2.6

The sentence on lines 172-173 doesn’t make sense to me. It should be re-written.

Table S3

The Genus column is redundant. It can be removed

3. Discussion

The discussion is shallow. The authors should expand on the meaning of the concepts and how they fit with other studies.

Line 195 – How can RNA editing change reading frames?

Line 211 – The final sentence is vague. How will the existence of this sequence help with future studies?

4. Materials and Methods

In general this section lacks detail and needs to be edited. As you consider how much detail to include ask yourself, “Could another scientist recreate my methodology?”

Suggested English language edits for the abstract and introduction. I have included this as an example of the level of editing required for much of the manuscript.

Line 9 – Pharmaceutical is misspelled

Line 13 – …genome of L. chinensewas sequenced…

Line 18 – …have the standard…

Line 21 – L. chinense is a sister taxon to…

Line 21 – In general, the complete…

Line 23 – …species, and phylogenetic…

Line 32 – …the dry root bark of L. chinenseis widely used…

Line 35 – …belongs to the Solanaceae family

Line 36 – …24 genera

Line 36 – ...among which Lycium is one of the most important.

Line 39 – …uniquely located…

Line 41 – DNA barcoding has been…

Line 42 – …analyze the phylogenetic relationships within the…

Line 45 – … (CP) genomes have…

Line 46 - …land plants. Chloroplasts play an indispensable role in a plant cell’s utilization of photosynthesis, carbon fixation, and… (plastids perform many roles important for plant cell physiology. I recommend the authors mention these)

Line 48 – …sequencing an entire genome is feasible for most laboratories…

Line 49 – According to published reports, the …

Line 50 – …are highly conserved with…

Lines 50-51 – You should explain what the IR and SC regions are.

Lines 51-53 – Chloroplast genomes can be used to study evolutionary relationships at a taxonomic level as a result of being maternally inherited, haploid, and highly conserved…

Line 55 – Transcriptome analysis of L. chinense leaves have…

Lines 56-58 – Here we report the CP genome of L. chinense based on next-generation…

Line 60 – To the best of our knowledge, this is the first comprehensive analysis of the CP…

Author Response

Dear reviewer:

Thank you so much for your advice. I have revised the article according to your advices.

Point 1：In this paper the authors announce the plastome sequence forLycium chinense, a species endemic to China that produces an edible fruit and is important in traditional Chinese herbology. The science and the methodology seem to be OK but the paper is not ready for publication. Numerous grammatical, sentence construction, and word choice errors occur throughout the paper. The authors should consider having a professor of English or a native English speaker review the text before they resubmit. In my comments below, I have provided some changes regarding how the information is presented but also some English language usage edits. This is not a complete list of edits, as it is out of the purview of a scientific reviewer to highly edit a paper for language usage to the degree that would be required to make this paper acceptable.

Response 1: Thank you so much for your advice. I am so sorry for this, And according to your advice，I have engage a professional to go over and correct the language and grammar of the paper.

Point 2：Line 28 – “at the magnificent” – the scientific primary literature shouldn’t include hyperbole in its descriptions of cultural traditions. I recommend, “Lycium chinense plays an important role in Chinese traditional medicine.”

Response 2: Thank you so much for your advice. And according to your advice，I have rewrite it.

Point 3：What makes this a “functional food”?

Response 3: Thank you so much for your advice. I think functional food refers to a food with a specific function, suitable for a specific group of people to eat, can adjust the function of the body, and not for the purpose of treatment. I have deleted this words from the manuscript, since It will produce ambiguity.

Point 4：Line 36 – “among which Lycium is one of the most important.” What makes this genus “important”?

Response 4: Thank you so much for your advice. According to the citation[7], the fruit, leaf, root bark, and young shoot of many species of the genus Lycium L. have long been used as local foods and/or medicines, so it is important.

Point 5：Lines 42-43 – These sentences contradict one another. The authors site a study where barcodes were effectively used to identify relationships in Lyciumbut then say they are not effective. Which is it?

Response 5: Thank you so much for your advice. I am so sorry, in this sentence my intended meaning is DNA barcoding was tried to identify and analysis the phylogenetic relationships of the Lycium genus, but it is not so effective. So it needs more effective methods.

Point 6：Beginning on line 97 there is a comparison of L. chinenseto other species. These other species and their relationship toL. chinensehas not been introduced or described making it difficult for the reader to understand its importance.

Response 6: Thank you so much for your advice. According to your advices, I introduced their relationship in the text, they belong to the same family.

Point 7：Line 99 – what is meant by “forward and palindromic”

Response 7: Thank you so much for your advice. Forward means forward repeat sequence，the direction of this repeat sequence is the same， and palindromic means palindromic repeat sequence，it is an inverted repeat in double-stranded DNA, and when the double strand of the sequence is opened, a hairpin structure can be formed. This sequence is called a palindrome sequence.

Point 8：The first paragraph, lines 146-154 is difficult to understand. The second sentence is non-sensical. I can’t tell if the difficulty I’m having is from the author’s English language usage or an incomplete description of the data. It should be rewritten.

Response 8: Thank you so much for your advice. According to your advices, it has been rewritten.

Point 9 ：The sentence on lines 172-173 doesn’t make sense to me. It should be re-written.

Response 9: Thank you so much for your advice. According to your advices, it has been rewritten.

Point 10 ：Table S3 The Genus column is redundant. It can be removed

Response 10: Thank you so much for your advice. According to your advices, it has been removed.

Point 11 ：The discussion is shallow. The authors should expand on the meaning of the concepts and how they fit with other studies.

Response 11: Thank you so much for your advice. And According to your advices, I have expand on the meaning of the concepts and how they fit with other studies.

Point 12 ：Line 195 – How can RNA editing change reading frames?

Response 12：Thank you so much for your question. I want to explain this，RNA editing is one of the post-transcriptional regulation mechanisms of gene expression in the chloroplast of higher plants, so it can change reading frames.

Point 13 ：Line 211 – The final sentence is vague. How will the existence of this sequence help with future studies?

Response 13：Thank you so much for your question. I want to explain this，What I want to say in this sentence is that this study can promote the identification of future species using the chloroplast genome, rather than saying that the existence of this sequence can promote any research.

Point 14 ：In general this section（Methods and materials）lacks detail and needs to be edited. As you consider how much detail to include ask yourself, “Could another scientist recreate my methodology?”

Response 14：Thank you so much for your advice. According to your advices, I have added details to this part.

Point 15 ：Suggested English language edits for the abstract and introduction. I have included this as an example of the level of editing required for much of the manuscript.

Response 15：Thank you so much for your advice. According to your advices, I have edited the article.

Line 9 – Pharmaceutical is misspelled