New Insights into Evolution of the ABC Transporter Family in Mesostigma viride, a Unicellular Charophyte Algae

Round 1

Reviewer 1 Report

This review is for the article “New Insights into Evolution of the ABC Transporter Family in 2 Plants Revealed by Unicellular Charophyte Algae” by Xiaoping Gong *, Shanhong Wang.

 

The work is an important study on the ABC transporter family evolution by analyzing plant species representing broad plant lineages, i.e., chlorophytes, charophytes, 14 bryophytes, lycophytes, gymnosperms, basal angiosperms, monocots, and eudicots. Especially, a previous investigation of ABCs in unicellular charophyte algae is lacking. The phylogenetic analyses to include Mesostigma viride is therefore critical to our understanding the functional evolution of the plant ABC family.

 

Material & Methods:

Lines 49-50: Please provide citations of these well-studied ABC proteins and discuss how the search for each subfamily was carried out.

 

Lines 68-70: Why did alternative methods such as ML and Bayesian approaches not be used to verify the resulting relationships?

 

In the Results and Discussion, the authors might consider clarifying their terminology early in the text using "groups" (G) to indicate the paralogs in each protein subfamily.

 

Fig. 8 legend to indicate what WBC, PDR stands for. In general, the figures need to be understandable without reference to the text.

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

In this manuscript, Gong and Wang review ABC transporters in charophyte algae, with an emphasis in Mesostigma viride. However, a recent review on the same topic:

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.17779

Has adressed this topic. I strongly recommend authors to make compartion of their data to this review, specially to figure 1 and Table 1. Moreover, authors must deliver a similar table in their manuscript. Did authors here arrive in the same number of the review? If not, which are the differences? I strongly recommend to include at least all charophyte and chlorophyte species of this above mentioned review in the present manuscript.

 

In terms of phylogenetic analyses, I strongly recommend authors to use  IQ-tree (http://iqtree.cibiv.univie.ac.at/), since it is a much more robust method than neighbor-joining with p-distance.

It is also important to clarify which domains authors used to check the retrieved transporters. For inspiration, the items 2.2 and 2.3 of this paper: https://www.mdpi.com/2073-4395/11/2/318/htm is a much better and elegant explanation and rationale to retrieve ABC transporters in Mesostigma viride and a more robust phylogenetic analysis.

Synteny analysis similar to Bavaresco et al (2021) (https://link.springer.com/article/10.1007/s12892-021-00130-4) in the item "Synteny analysis and evolutionary analysis" should also be run.

 

If avaliable, public RNA-seq data should also be used to estimate gene expression in  Mesostigma viride.

Some recent reviews in plant ABC transporters, such as:
https://doi.org/10.1016/j.pbi.2017.08.003

https://doi.org/10.1093/jxb/eraa260

https://doi.org/10.1016/j.phytochem.2021.112663

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.17779

Should also be carefully read and added in Introduction.

Overall, the manuscript is well written; however, it lacks several more analyses to in fact be accepted.

Author Response

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Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

In this new version, Gong and Wang made some improvements compared to the first version.

One remark in Introduction: Since authors claim in the title that this paper focus on Charophyte Algae, it is important to state: how many charophyte algae genome were sequenced? How many were used here? This information with proper citations would be importante.

Regarding Response 1:

Banasiak and Jasiński paper did not give IDs, but they gave numbers. Are numbers comparable between that revision and this paper?

I completely understand that phylogenetic analysis is timing consuming; however, in this paper, that was the only experiment made. So, it is important to have strong analyses in this part.

Authors want to focus their analyses in charophyte algae which is indeed a good justification. However only 2 out of 11 analysed genomes (less than 20%) were in fact charophytes. I would strongly recommend to include Chlorokybus atmophyticus genome (https://phycocosm.jgi.doe.gov/Chlat1/Chlat1.home.html) and also consider the inclusion of Mesotaenium endlicherianum (https://phycocosm.jgi.doe.gov/Mesen1/Mesen1.home.html), Spirogloea muscicola (https://phycocosm.jgi.doe.gov/Spimu1/Spimu1.home.html) and Chara braunii (https://phycocosm.jgi.doe.gov/Chabra1/Chabra1.home.html) genomes, in order to have a more "balanced" analysis in favor of neglected algal genomes. Another solution is to focus manuscript title in M. viride genome.

 

Regarding response 3

Please, include pfam codes for (TMD-NBD) domain; the same for all used CDD domains.

 

Regarding response 4

The analysis was expected to be done among charophyte algae.

 

Regarding response 5

Which genes were not expressed? Which was the level of expression in RNA-seq data? Please, detail this in results and how it was analyzed in methods

 

After these modifications, the paper can be reanalyzed.

Author Response

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Author Response File: Author Response.docx

Round 3

Reviewer 2 Report

In this new version, most improvements were done.

I have only a few remarks:

1- I very strongly advise to change the title of the manuscript to: "New Insights into Evolution of the ABC Transporter Family in Mesostigma
viride,  a Unicellular Charophyte Algae"

 

2- line 52: "that have available genomes" should be suppressed. Much more plants have available genomes, including Algae.

3- line 69: change "will be" to "were"

4- line 80-83: the GEO accession do not have expression profiles, just the raw data. How authors could retrieve leves of expression to make th heatmap? Please, put this explanation in this topic. Authors should also mention which R package was used for creating the heatmap.

 

5- line 295: substitute "unicellular charophyte algae and representative species." to "Mesostigma viride."

 

After these mandatory changes, the article can be accepted.

 

 

Author Response

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Author Response File: Author Response.pdf