PONE-D-21-33675Complete chloroplast genomes of Asparagus aethiopicus L., Asparagus densiflorus (Kunth) Jessop ‘Myers’ & Asparagus cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congeneric speciesPLOS ONE

Dear Dr. LAU,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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As suggested by Reviewer #1, literature update is highly recommended, as the authors did not present the latest findings related to the scientific matter. Moreover, an in depth authors' elaboration of the present text regarding the literature update is expected.

The whole text would hugely benefit if proofread by a native English speaker or a professional editing agency. Some but not all places of much needed intervention are following:

L36: "species" should not stand italicized.

L39: "Asparagus have been widely applied..." - a colloquial expression. Suggestion: "Many species belonging to the Asparagus genus have been widely applied..."

L41, L58 and elsewhere in the text: "anthropocentric usage of Asparagus", "while some Asparagus were used"... - the same comment as the previous.

L47 and further in the text: Please use "A." to abbreviate the genus name when introducing a species name.

L77 and elsewhere in the text: Do not capitalize common plant names such as "Garden Asparagus". Write "garden asparagus".

Please note that Reviewer #2 has stated "...I have labelled these shortcomings in this paper;..." but did not provide the attachment where these shortcomings might be visible. The reviewer remains unresponsive regarding this issue.

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Branislav T. Šiler, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

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Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The Authors have carried out a study based on the sequencing of the Complete Chloroplast Genome of three species (A. aethiopicus, A. densiflorus ‘Myers’ and A. cochinchinensis) belonging to the Asparagus genus. The results obtained were assembled with chloroplast genomes of other four Asparagus species (A. setaceus, A. racemosus, A. schoberioides Asparagus officinalis L.) on NCBI. The manuscript could bring a significative impact for further studies aimed to widen the knowledge of the Asparagus genus and the phylogenetic relationships among Asparagus spp. In my opinion, the paper could be published after a few modifications that might improve this manuscript.

The main criticism to this paper is that I have lacked the mention of some studies employing cpDNA that have been previously developed in the Asparagus genus ( Lee et al 1996; Lee et al 1997; Kanno et al 1997; Seng et al 2017 and Li et al 2019). I was impressed about the comprehensive and detailed revision on the taxonomic classifications in the asparagus genus that have been published since the eighteen century to date. However, previous studies employing cpDNA of different Asparagus spp. are not mentioned in the manuscript. In my opinion these studies should be mentioned in the Introduction section of the manuscript. I think that at least the studies developed by Lee et al. (1997) and Seng et al. (2017) are recommended to be also used in the discussion of the manuscript because the findings of the present study can be compared to a certain extent with the obtained by these two studies.

Other comments and suggestions for the Authors:

> Abstract: The authors wrote: “Conducting comparative and phylogenetic analysis with congeneric species, four cpDNA on NCBI were included in this study”. The scientific name of these four species (A. setaceus, A. racemosus, A. schoberioides Asparagus officinalis L.) they should be included in this section of the manuscript.

> lines 35-37: In these lines is written the following sentence: “These aforementioned characteristics were evolved by Asparagus species to adapt to arid environment”. I think that this sentence must be support by a cite/s

> lines 43-44: It is written: “of the two studied Asparagus species were discussed in detail” Is it correct? Two (A. aethiopicus, A. densiflorus ‘Myers’) or three species (A. aethiopicus, A. densiflorus ‘Myers’, A. cochinchinensis)?

> Lines 78- 79. The authors wrote: “However, the gene pool of A. officinalis is relatively limited” In my opinion there are other studies such as Geoffriau et al 1992, Moreno et al 2006 or Mercati et al 2015 that must be cited instead of the study carried out by Stajner et al 2002

> lines 79-80: I suggest modifying the following sentence: “The species is susceptible to multiple diseases” by the species is susceptible to multiple biotic and abiotic stresses…

Lee, Y. O., Kanno, A., & Kameya, T. (1997). Phylogenetic relationships in the genus Asparagus based on the restriction enzyme analysis of the chloroplast DNA. Japanese Journal of Breeding, 47(4), 375-378.

Sheng, W., Chai, X., Rao, Y., Tu, X., & Du, S. (2017). Complete chloroplast genome sequence of Asparagus (asparagus officinalis l.) and its phylogenetic position within asparagales. Journal of Plant Breeding and Genetics, 5(3), 121-128.

Lee, Y. O., Kanno, A., & Kameya, T. (1996). The physical map of the chloroplast DNA from Asparagus officinalis L. Theoretical and Applied Genetics, 92(1), 10-14.

Kanno, A., Lee, Y. O., & Kameya, T. (1997). The structure of the chloroplast genome in members of the genus Asparagus. Theoretical and applied genetics, 95(8), 1196-1202.

Li, J. R., Li, S. F., Wang, J., Dong, R., Zhu, H. W., Li, N., ... & Gao, W. J. (2019). Characterization of the complete chloroplast genome of Asparagus setaceus. Mitochondrial DNA Part B, 4(2), 2639-2640.

Moreno, R., Espejo, J. A., Cabrera, A., Millan, T., & Gil, J. (2006). Ploidic and molecular analysis of ‘Morado de Huetor’asparagus (Asparagus officinale L.) population; a Spanish tetraploid landrace. Genetic Resources and Crop Evolution, 53(4), 729-736.

Geoffriau E, Denoue D, Rameau C (1992) Assessment of genetic variation among asparagus (Asparagus officinalis L.) populations and cultivars: agromorphological and isozymic data. Euphytica 61(3):169–179

Mercati F, Riccardi P, Harkess A et al (2015) Single nucleotide polymorphism–based parentage analysis and population structure in garden asparagus, a worldwide genetic stock classification. Mol Breed 35(2):59.

Reviewer #2: The introduction part is chaotic in this manuscript, which shoule be rewritten；Please pay attention to some mistakes in your grammar and spelling, and I have labelled these shortcomings in this paper; the content is complete, and the result is clear; and I suggest this paper should be accepted after minor revison.

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Reviewer #1: No

Reviewer #2: Yes: Wentao Sheng

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PONE-D-21-33675R1Complete chloroplast genomes of Asparagus aethiopicus L., Asparagus densiflorus (Kunth) Jessop ‘Myers’ & Asparagus cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congeneric speciesPLOS ONE

Dear Dr. LAU,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================

Following the rules of ICN (not ICNCP, since the studied taxa are not cultivated) is absolutely necessary in scientific literature and I fully support it. However, please bear in mind that abbreviating genus name does not oppose the ICN rules (the current version is Shenzhen Code, published by IAPT - https://www.iapt-taxon.org/nomen/main.php; for genera, please see https://www.iapt-taxon.org/nomen/pages/main/art_20.html). It is a common scientific practice to write a scientific name in full when it is first used or when several species from the same genus are being listed or discussed in the same paper or report. For subsequent uses, the genus can be abbreviated to its first letter followed by a period. You can abbreviate the genus name after its first use even when describing a different species within that genus, as long as there is no risk of confusing it for another genus or genera (which is not the case here, since only the genus Asparagus circulates throughout the manuscript). Therefore, by abbreviating the genus name (i) obeying the rules of ICN is not compromised, ii) nomenclatural treatment is presented accurately (no confusion to other genera starting with "A."), and iii) if a species is described in a source article as e.g., "Asparagus aethiopicus", I do not see the reason why in consequent articles dealing with the same species it wouldn't be abbreviated as "A. aethiopicus" if the genus name was already mentioned earlier in the text. The same applies to the main title: reprising the genus name three times is space-consuming and quite exhausting for reading. I suggest abbreviating here the genus name for the second and the third species as well (also, replace "&" with "and" here and elsewhere in the text). The exceptions might be L178-179 (cites the original text), L197-200 (cites the original text), L218-220 (only for mentioning Asparagus myersii, since a binomial name has been announced), L222-223 (cites the original text), Table 1, L614-616 (a full name has been announced), L647-648 (as it complies with the ICN rules), L649-651 (but being the common name, "asparagus” should stand in lowercase).

Moreover, vernacular expressions such as L101 (circumscription of Asparagus), L117 (relationships within Asparagus), L125 (only one native Asparagus), L126 (Other common exotic Asparagus), L232 (7 Asparagus were examined) (and in many other places) were not clarified as required in the previous review round.

102-107: The terms "genus" and "subgenus" should stand in lowercase.

L127-129 and elsewhere in the text: I must repeat: common names should be written in lowercase, i.e., "sprengeri asparagus" (however, I'm not aware of this Latinized common name, but "Sprenger's asparagus" might be acceptable, after Carl Ludwig Sprenger), "lace fern", etc.

The authors are urged to meticulously check the text once again for proper English usage while following the comments stated above. I still strongly encourage the authors to have the MS proofread by a native English speaker or professional editing agency.

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Please submit your revised manuscript by Mar 17 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
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We look forward to receiving your revised manuscript.

Kind regards,

Branislav T. Šiler, Ph.D.

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Complete chloroplast genomes of Asparagus aethiopicus L., A. densiflorus (Kunth) Jessop ‘Myers’, and A. cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congenerics

PONE-D-21-33675R2

Dear Dr. LAU,

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Branislav T. Šiler, Ph.D.

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PLOS ONE

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