Comparative Study of Plastomes in Solanum tuberosum with Different Cytoplasm Types
, Evgeniia Sotnikova 2, Alexey Meleshin 1, Natalia Gaitova 1, Anna Egorova 1, Anatoly Semenov 1, Ekaterina Gins 1, Alina Koroleva 1, Evgeny Moskalev 1, Elena Oves 1, Oleg Kazakov 1, Aleksey Troitsky 3,* and Denis Goryunov 1,3,*Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsIn this manuscript, Goryunova et al. present their study on sequencing the chloroplast genomes of five cytoplasmic types of Solanum tuberosum and their comparison. They characterize their genomic content and present their phylogenetic affiliations and divergence times. They also perform an adaptive evolution analysis based on the Ka to Ks ratio.
The paper is very well written, providing thorough background information, using the appropriate methodology, and clearly presenting the results and discussion. Please find below a couple of minor comments about the wording:
L16: Please replace "... 6 types of potato cytoplasm..." with "... 6 cytoplasm(ic) types in potato..." OR "potato cytoplasm types" for better English.
L. 37: Same as above.
L. 95: Pls, replace "Chili" with "Chile".
L. 306. There is no reference to Figure 6 in the body text. This line could be the appropriate place to do so.
L. 340, Figure 6. Pls, mark the major groups and subgroups using readable font, as the existing annotations on the clade tips are indistinguishable.
L. 615: Pls, remove the period mark (".") after "genome sequencing".
Author Response
Dear reviewer,
We are grateful for thorough reading of our manuscript and providing comments to improve its quality. Please find our replies below.
REVIEWER 1
In this manuscript, Goryunova et al. present their study on sequencing the chloroplast genomes of five cytoplasmic types of Solanum tuberosum and their comparison. They characterize their genomic content and present their phylogenetic affiliations and divergence times. They also perform an adaptive evolution analysis based on the Ka to Ks ratio.
The paper is very well written, providing thorough background information, using the appropriate methodology, and clearly presenting the results and discussion. Please find below a couple of minor comments about the wording:
L16: Please replace "... 6 types of potato cytoplasm..." with "... 6 cytoplasm(ic) types in potato..." OR "potato cytoplasm types" for better English.
Corrected.
- 37: Same as above.
Corrected.
- 95: Pls, replace "Chili" with "Chile".
Corrected.
- 306. There is no reference to Figure 6 in the body text. This line could be the appropriate place to do so.
Corrected.
- 340, Figure 6. Pls, mark the major groups and subgroups using readable font, as the existing annotations on the clade tips are indistinguishable.
Major groups and subgroups are indicated.
- 615: Pls, remove the period mark (".") after "genome sequencing".
Corrected.
Reviewer 2 Report
Comments and Suggestions for AuthorsReview of Goryunova et al.
Comparative study of Plastomes of Solanum tuberosum with different cytoplasm types.
The manuscript contains new and important information. However, the focus on cytoplasmic relationships to the plastome is not clear. The authors selected to sequence chloroplast genomes from a selection of cytoplasmic types (A,P,T, D, W) and then sequenced chloroplast genomes. There is no mention of the mitochondrial contribution to the cytoplasmic background.
The data presented does demonstrate some level of diversity in chloroplast genomes found in Solanum and adds to the literate already published. The author’s way of presenting the data as cytoplasmic and not a comparison between chloroplast genomes is odd.
Table 1: Figure legend should define heading particularly IR, LSC, SSC.
Figure 1: Legend needs to be more informative.
Figure 3: Legend needs more information. Define LSC, IRb, SSC, IRa and the Roman numerals.
Figure 5 is unclear. Accession from the author’s work is marked with an asterisk but it is so small that it is difficult to identify.
Figure 6: This has the same issues as Figure 5. The asterisk is too small. It would also benefit the figure if some of the major branches could be labeled and identified.
Comments on the Quality of English LanguageMinor edits needed, generally well written.
Author Response
We are grateful for thorough reading of our manuscript and providing comments to improve its quality. Please find our replies below.
REVIEWER 2
The manuscript contains new and important information. However, the focus on cytoplasmic relationships to the plastome is not clear. The authors selected to sequence chloroplast genomes from a selection of cytoplasmic types (A,P,T, D, W) and then sequenced chloroplast genomes. There is no mention of the mitochondrial contribution to the cytoplasmic background.
The data presented does demonstrate some level of diversity in chloroplast genomes found in Solanum and adds to the literate already published. The author’s way of presenting the data as cytoplasmic and not a comparison between chloroplast genomes is odd.
Table 1: Figure legend should define heading particularly IR, LSC, SSC.
Corrected.Figure 1: Legend needs to be more informative.
Additional information has been included.
Figure 3: Legend needs more information. Define LSC, IRb, SSC, IRa and the Roman numerals.
Information regarding LSC, IRb, SSC, IRa and the Roman numerals is included. In addition, LSC, SSC and IRs abbreviations were explained in the manuscript body (L 166-168). Peaks number were introduced in the manuscript body as well
Figure 5 is unclear. Accession from the author’s work is marked with an asterisk but it is so small that it is difficult to identify.
Asterisks are enlarged.
Figure 6: This has the same issues as Figure 5. The asterisk is too small. It would also benefit the figure if some of the major branches could be labeled and identified.
Asterisks are enlarged. Major branches are labeled.
Comments on the Quality of English Language
Minor edits needed, generally well written.
We checked the text once more.
