Transcriptomic Approach for Investigation of Solanum spp. Resistance upon Early-Stage Broomrape Parasitism
, Vasiliki Kotsira 2,3, Aliki Kapazoglou 4, Spyros Tastsoglou 2,3, Anastasios Katsileros 1, Demosthenis Chachalis 5, Artemis G. Hatzigeorgiou 2,3,* and Eleni Tani 1,*Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors apply transcriptomics to study the early-stage interaction between the parasitic weed broomrape and both commercial and introgression lines of tomato. Key genes and metabolic pathways were analyzed and discussed (the Discussion section is well-written). I recommend this paper for publication, with some minor adjustments to the text and figures.
Minor issues:
1. Numerous missing marks or typos are present in the text. There are unexplained parentheses in lines 207 and 216; missing spaces in lines 257, 292, 374, 375, 394, 475, and Table 1; an extra space in line 245; a confusion between "plans" or "plants" in line 288; and an extraneous symbol ")" in line 433.
2. In this study, the introgression lines originate from Eshed's work (Ref 29, 1995). I ask the authors to mention some existing alternative or more recent lines and underline the advantages of the used plant lines.
3. Results, section 3.1 It's up to the authors, but photos of parasitized, partially parasitized, and non-parasitized roots would be very welcome. This is not a critical point, so it is left to the authors' discretion whether to add the photos or not.
4. Figure 2: The panels in this figure are too close together, and the axis labels are too close to other panels. Please space each of the panels further apart or separate the panels with lines.
5. Figure 3: The labels on the right side of panels B and C are pixelated (low resolution) and unreadable.
6. Figure 4: The zero is missing on the Y-axis in panels C, D, and F.
7. Figure 4 and Figure 5 legends: "Statistically significant differences were determined…" Differences compared to which control?
8. Line 633: The symbol for HFRI may be is non-allowed in the text.
Author Response
- Comment: Numerous missing marks or typos are present in the text. There are unexplained parentheses in lines 207 and 216; missing spaces in lines 257, 292, 374, 375, 394, 475, and Table 1; an extra space in line 245; a confusion between "plans" or "plants" in line 288; and an extraneous symbol ")" in line 433.
Response: We would like to thank the reviewer for the comments! The numerous missing marks and typos have been corrected in the manuscript according to their suggestions.
- Comment: In this study, the introgression lines originate from Eshed's work (Ref 29, 1995). I ask the authors to mention some existing alternative or more recent lines and underline the advantages of the used plant lines.
Response: We appreciate the reviewer’s comment. Eshed and Zamir in 1995 developed a large number of ILs by crossing S.lycopersicum & S.pennelli species. These ILs have been extensively studied through all these years for numerous research reasons and applications, however, to our knowledge, there are no alternative or more recent lines developed and studied yet today regarding the combination of these two species. The advantages regarding the ILs use were added in the manuscript (Lines: 97-105).
Daniel H. Chitwood, Ravi Kumar, Lauren R. Headland, Aashish Ranjan, Michael F. Covington, Yasunori Ichihashi, Daniel Fulop, José M. Jiménez-Gómez, Jie Peng, Julin N. Maloof, Neelima R. Sinha, A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines , The Plant Cell, Volume 25, Issue 7, July 2013, Pages 2465–2481, https://doi.org/10.1105/tpc.113.112391
- Comment:Results, section 3.1 It's up to the authors, but photos of parasitized, partially parasitized, and non-parasitized roots would be very welcome. This is not a critical point, so it is left to the authors' discretion whether to add the photos or not.
Response: Figure 1 from supplementary data was added to the manuscript as proposed by the reviewer.
- Comment: Figure 2: The panels in this figure are too close together, and the axis labels are too close to other panels. Please space each of the panels further apart or separate the panels with lines.
Response: We thank the reviewer for that comment. The panels in the new Figure 3 (old version 2) have been corrected accordingly.
- Comment:Figure 3: The labels on the right side of panels B and C are pixelated (low resolution) and unreadable.
Response: We would like to thank the reviewer for the comment. Panels were modified accordingly.
- Comment:Figure 4: The zero is missing on the Y-axis in panels C, D, and F.
Response: New Figure five (old 4) has been modified according to the reviewer’s comment.
- Comment: Figure 4 and Figure 5 legends: "Statistically significant differences were determined…" Differences compared to which control?
Response: We would like to thank the reviewer for the comment. The statistically significant differences were determined by comparing the relative expression between control and parasitized plants/genotype.
- Comment: Line 633: The symbol for HFRI may be is non-allowed in the text.
Response: The symbol for HFRI was removed.
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors provide novel evidence investigating the early-stage infection of tomato with the parasitic organism P. ramosa. The novelty of this study stems from the approach and timing of sampling leading to the identification of differentially expressed genes and metabolic pathways operating in the host roots in response to infection. Ultimately findings from this study will allow for developing molecular markers and pinpointing target genes for detecting, minting and optimising the establishing of tomato resistance to P. ramosa.
Minor suggestions for improvement:
1. Please state major conclusions in the abstract regarding the transcriptomic analysis (currently too vague).
2. May not be essential to justify the use of RNAseq and PEA in the manuscript (Lines 91-99)
3. Please state the quantity of RNA used (ng?) for RNAseq and number of replicates.
4. Perhaps the authors could include Supp. Figure 1 in the main manuscript to show images of the parasitised plants.
Author Response
- Comment: Please state major conclusions in the abstract regarding the transcriptomic analysis (currently too vague).
Response:We appreciate the reviewer’s comment. Modifications have been applied in the abstract accordingly.
- Comment: May not be essential to justify the use of RNAseq and PEA in the manuscript (Lines 91-99)
Response:We appreciate the reviewer’s comment. We believe that a brief reference to these two techniques enhances the understanding and concept of the experimental procedure, for these reasons we prefer to keep lines 91-99.
- Comment: Please state the quantity of RNA used (ng?) for RNAseq and number of replicates.
Response:We would like to thank the reviewer for the comment. The RNA sample details were added in the manuscript (Lines 172-174: “. Each sample had concentrations between 85 ng/uL to 260 ng/uL and six biological replicates (three control plants and three parasitized plants) for each genotype were sequenced.”)
- Comment: Perhaps the authors could include Supp. Figure 1 in the main manuscript to show images of the parasitized plants.
Response: Figure 1 from supplementary data was added as proposed by the reviewer.
