Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses

Round 1

Reviewer 1 Report

The manuscript presents studies leading to genome-wide identification of gene family coding dirigent (DIR) proteins in the eggplant genome and determination of gene-expression patterns under some abiotic (3) and a biotic stresses (3).

The results were obtained using bioinformatics and data from earlier publications.

The DIR genes are involved in synthesis of lignin and lignans which undergo tissues specific and environmental control providing  tolerance/ protection against unfavourite environmental conditions and thus crucial for crop production (putative genetic markers are proposed for potential applications in breeding of eggplants).

The studies show novelty with respect of the species taken as the objective. Manuscript is generally well designed and written. The paper presents, in my opinion, high scientific quality, where modern bioinformatics techniques are used. Unfortunately I not expert in details of the methodical approach, and thus unable to evaluate the correctness of applied procedures. 

The manuscript requires some editorial corrections, exemplified by 

line 15 ...... in the biosynthesis of lignans and lignans......  ?   

line 51 .... "Besides, lignans can also  ?   against insect attacks by .....  

line 395 ..."bule color" ....

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

The presented article «Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses» is devoted to important and topical problems of modern molecular biology. In particular, the authors identified 24 genes encoding dirigent (DIR) proteins in eggplant by molecular and bioinformatic approaches. Additionally, expression pattern of these genes under different abiotic and biotic stresses has been studied. Experimental data is relevant and has novelty. This article is of great interest to the world scientific community. However, unfortunately, there are both insignificant and significant remarks, as well as issues that should be taken into account.

insignificant remarks

1)     Add of the author-classifier to the genus and species names plants. In addition, for the first time in the text, the generic name should be presented in full (for example, Arabidopsis thaliana (L.) Heynh.), while further in the text it should be abbreviated (for example, A.).

2)     All genes should be written in italics, including gene families (DIR genes) and subfamilies (DIR-a, DIR-b/d, and DIR-e).

3)     Line 15. lignans and lignans → lignins and lignans?

4)     Be careful when abbreviations are first mentioned, such as JA, SA, and ABA (line 67). Abbreviations at the first mention should be written in full and decoded.

significant remarks

1.     Figures 3, 5, 7 and 8 are of poor quality. Figures are not readable.

2.     The authors approve that they have studied the tissue-specific expression pattern of 19 DIR genes. However, this statement is extremely incorrect, since in the experiment the authors used not specific tissues, but organs or their fragments (lines 142-143 cotyledon, radicle, root, stem, flower, pistil, leaf, bud, fruit peduncle, fruit skin, fruit flesh, fruit). Cotyledon, root, stem, flower, leaf and other contain different tissues. Organ-specific expression is more correct.

3.     The authors do not specify which eggplant cultivars or line were used. Maybe there were a lot of them?

4.     The authors do not comment on the creation of stressful conditions in the materials and methods section. I'm not clear if these were in vitro or ex vitro plants? What age were the donor plants? What temperature has been used for low temperature stress? The same applies to high temperature stress. How was salt stress simulated (factor and its concentration)? How was sampling of plant material carried out for expression analysis? All of these factors are extremely important and fundamental for molecular research.

5.     The authors conduct a comparative synteny analysis of DIR genes among eggplant, Arabidopsis thaliana (L.) Heynh and rice. Generally, this is correct, since a comparison is made with distant monocots and model dicots with a sequenced genome. However, it is quite clear to me why the authors do not make a comparison with the DIR genes of a closely related tomato? There is a modern article on the genome-wide computational analysis of tomato DIR genes (Saddique, M. A. B. (2022). Genome-wide Computational Analysis of DIR Genes in Solanum lycopersicum. https://assets.researchsquare.com/files/rs-1617785/v1/899faa78-7525-46ff-91fb-2c8a0a923f52.pdf?c=1652290133). Such a comparison of the DIR genes of eggplant and tomato would be extremely interesting and useful, since both of them are members of the Solanum genus. Unfortunately, this information is not available in the Introduction and Discussion sections.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

Dear Authors,

Thank you for your comments and corrections. I recommend the resubmitted article for publication in the Horticulturae journal. 

Best regards,

reviewer