Lily Database: A Comprehensive Genomic Resource for the Liliaceae Family

Round 1

Reviewer 1 Report

In the article "Lily Database: A Comprehensive Genomic Resource for the Liliaceae Family," the authors have developed a database incorporating RNA-seq, TF data, and marker information. This is my second review of this manuscript, and it still exhibits numerous shortcomings. In the revised manuscript, the authors have addressed some of my previous concerns by modifying parts of the database and the article. However, I had requested provided the SRA numbers for the RNA-data used from NCBI, which the authors have not included in this revision. The manuscript also lacks a "data availability" section, meaning the authors' sequenced RNA-seq data is not publicly available in common databases. As an open access journal, data openness is essential. The logic in the web database's "Lily Genotype Search" is still unclear. Without a clear understanding of the resources available, the "Cultivar Name" does not offer a referential list, and the relationship between "Cultivar Name" and "group" is ambiguous. It is unclear whether one should first provide a "Cultivar Name" before selecting a corresponding "group", or if they operate independently. The authors have provided no clarification in this aspect. Moreover, when attempting to search using only "Group" and then separately searching the "Cultivar Name" within a group, I encountered no results, leading to a very poor user experience. Such illogical search patterns are prevalent throughout the database, and not all readers are database developers equipped to understand this inherent logic and search methodology. In the "Download" section, there are only two PDFs which,  upon attempting to access, show a 404 not found error.

Author Response

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Reviewer 2 Report

Thank you to the authors for their efforts. They have successfully addressed many of my earlier concerns. Nonetheless, a few areas still present some confusion or room for improvement:

1. The manuscript states that a total of 47,863 primers were designed from RNA sequence data and 103,929 primer pairs from genome assembly for the SSR marker database. I wonder if there’s any overlap between the primers derived from RNA sequences and those from genome assembly.

2. The classification of SNPs into transitions and Transversions was clear, and the manuscript notes that transitions are slightly more prevalent (line 240-243). However, Figure 2a seems to illustrate the contrary. Could the authors review this to ensure the data is represented accurately?

3. The text describes three Lilium genotypes subjected to various treatments for RNA sequencing, including L. longiflorum Easter, L. longiflorum White, and L. formolongi Sinnapal. However, I couldn't find the details for L. longiflorum White in Table S1. Also, what roles do the library L4-7 and L4-104 play in this study?

4. On line 204, there's a mention of "SSR markers were mined from seven datasets," but shouldn't it include the genome assembly as well, making it eight datasets?

1. Line 30, “et al, [2]” should be replaced by ““et al [2],”.

2. The sentence spanning lines 92-96 is quite lengthy and could be made clearer by splitting it. For instance: "This study utilized one genome assembly of Lilium candidum (Accession: GCA_031763035.1) and seven distinct RNA sequence datasets. Four RNA sequence datasets, along with the genome assembly, were sourced from the NCBI database. The remaining three RNA sequence datasets came from RNA-sequencing libraries prepared from different Lilium species genotypes, each subjected to unique treatment conditions as detailed in Table S1."

3. Line 202, “database features:” should be replaced by “database features”.

Author Response

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Reviewer 3 Report

The abstract section is written in the form of a commercial, is should be in more academic language.

The introduction section is full of errors and typos. 

The aim of the research does not match the title and the text.  What so you mean by 'develop genomic resources for the Lilium sp'? when you are not working on the actual resources but the online databases? Are you developing a database or a genetic resource base? Be very specific when choosing English terms, to avoid confusion. 

Leaf samples from greenhouse-grown plants presented in the table 1. 

Table 2 must be supplemented with the references used. 

Figure 1 should be redesigned to be placed as a graphical abstract, not a figure. 

In the results and discussion section, there is a complete absence of a substantial discussion and only one reference is cited. 

English needs editing. 

Author Response

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Reviewer 4 Report

The work aims the establishment of Lily database.

It's an interesting initiative regards to the high value ornamental plant which presents Lilium. I hope, this data base will be started and developed.

However, the Autors should develop methods because this paragraph is superficially written.

The tables and figures, also supplemental materials are correct. However, their area / edition should be corrected to the properly place (1 page table 2). 

I hope, in the Lily database we can read more as in conclusions is presented. 

Author Response

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Reviewer 5 Report

This is a very interesting work, and the author's efforts in this work are highly beneficial for future research on lilies. The website is aesthetically pleasing, concise, and both visualizations and searches are convenient. This will greatly contribute to the advancement of lily research. I believe this work is worthy of acceptance. However, some issues warrant discussion.

1, Line 102: The versions of Trinity and RSEM, including several versions of the software, are not mentioned in the manuscript.

2. Line 149: Although you mention the PlantTFDB v5.0, the paper seems to have not been cited.

3. 156-168 The selection of DEGs does not mention the software used.

Author Response

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Round 2

Reviewer 1 Report

The Authors have addressed all of my concerns with the revised manuscript. The revised manuscript is ready for publication.

Reviewer 3 Report

N/A