Combined Transcriptomic and Metabolomic Analysis Reveals the Mechanism of Flavonoid Biosynthesis in Handroanthus chrysanthus (Jacq.) S.O.Grose

Round 1

Reviewer 1 Report

The article is devoted to the study of secondary metabolites in Tabebuia chrysantha (Jaq.) using metabolomic and transcriptomic approaches. The performed analysis made it possible to identify a wide range of metabolites, including flavonoids, and to reveal the genes involved in the biosynthesis process. The results obtained greatly enrich knowledge on the secondary metabolites of T. chrysantha and are of potential practical value. However, the manuscript needs revision before it is suitable for publication.

Lines 80-81. How reasonable is it to combine bark material from different parts of the trunk? Won't they have different metabolic and transcriptome patterns and won't this give erroneous results?

Line 413. The sentence starts but does not end

Lines 477-479. The greater diversity of metabolites in the bark is not the reason why there are different metabolites in the bark and in the leaves. Please reformulate the proposal. Did the pooling of material from different parts of the trunk affect the high diversity of metabolites in this tissue?

Lines 542-556. Please rewrite the ‘conclusions’ section, shortening the description of technical data such as the number of genes and metabolites, adding more general biological conclusions, such as suggestions about which genes and metabolites might be potential targets for plant improvement.

Please check the numbering of the Figures. The Figure 2 and Figure 8 are absent; however, there are two Figure 3 and Figure 4.

The manuscript is negligently formatted, and English language is need to be improved.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

 

The study is overall, well planned and executed with sound data analysis and provides basic information on the specific pathway.

As a future research, identification of the bonafide candidate gene should be considered, since most of the biosynthetic genes exist as isoforms. It would be prudential to conduct co expression analysis with the exact candidate gene of the pathway, instead of designing qPCR primers based on conserved sequences from public domain. If whole genome sequences are available it would be easy, if not you have to clone individual isoforms based on the transcripts from your RNA seq data and then clone the isoforms to identify the variable regions for specific primer design for the candidate gene. If co expression analysis is done based on the right candidate gene, it becomes lot more easier to identify all the gene components of the pathway as well as related pathways.

Line no. 50- extract has

Line no. 62-64- re draft the sentence for clarity

Line no. 81- change Taked to taken, redraft the sentence for clarity

 

What were the genes used for normalization in qRT-PCR analysis, provide brief details or reference related to gene optimization. Whether you have optimised in both leaf and bark tissues?

 

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

The manuscript can be accepted.