Identification and Characterization of the Detoxification Genes Based on the Transcriptome of Tomicus yunnanensis

Round 1

Reviewer 1 Report

Identification and characterization of the detoxification genes based on the transcriptome of Tomicus yunnanensis

Authors have studied the transcriptome of male and female tissues including the heads, antenna, and legs of the bark beetle, Tomicus yunnanensis to identify the detoxification genes present in these tissues and also validate their expression profiles using qPCR.

The study provides significant knowledge on the bark beetle physiology and adds to the repertoire of the transcriptome studies of wood boring beetles. However, the authors have not taken complete advantage of the study they have performed. One of the major concerns is the lack of differential expression analysis between the different treatment which can contribute to profound differences in the sex and tissue specific detoxification gene profiles. The manuscript can be improved on sentence structure, word choice, and missing methodological details.

Manuscript will be acceptable for publication after the author address the following suggestions.

 

Line 45: Expand then name of the enzymes and include the abbreviations in parenthesis

Line 50: Replace xenogenic with xenobiotics

Line 55: This sentence is confusing. Why was the response to bacterial invasion included in this sentence?

Line 58: Elaborate on “variety”

Line 60: What includes particulate system?

Line 64: rephrase the sentence to be clear on the mode of action of GSTs on toxic compounds. This sentence can be split in to two if the authors would like to emphasize on the mechanism of action of GSTs

Line 70: Do odors represent volatiles? If so, do insects have volatiles? Rephrase accordingly

Line 73: How does feeing on two distinct regions of the plants represent two periods?

Line 78: Do adult worms move back to the top?

Line 95: How many adults were collected and the number of adults used for dissections. Were they all collected from the same region? Are there any biological replicates?

Line 97: replace feet with legs. Also, how were the insects transported from the collection site to the laboratory?

Line 118: Which program was used to process the raw reads?

Line 120: Include the version of Trinity For example the current version of Trinity is v.2.13.2

Line 123: Why were FPKM values generated?

Line 134: Was the blast done in NCBI Blast+ standalone blast program?

Line 150: Replace residue with carcass. Include details of the sample collection site per biological replicate, the number of insects used for gene expression analysis. Number of biological replicates included (move it from line 154 to here).

Line 155: Concentration of the primer

Line 156: What was the stability of the internal control across all the treatments?

Line 166: Description of the male and female samples was not provided in the methods

Line 162: Perform a BUSCO analysis to determine the completeness of the transcriptome.

Line 179: Which six databases. This approach was not included in the methods

Line 184: Scientific names are not italicized also there is a typo in Nephila clavipes

Line 179: Which program as used to annotate the transcripts? Also replace “unigenes” with transcripts. Were the redundant transcripts removed by any program?

Line 191: How was the GO analysis performed? Need to include these in the methods.

Line 197: Expand KOG

Line 204: Please explain “Overview” pathway

Line 219: Methods mention removal of sequences with less than 50 amino acids which is different than the number mentioned here. Please clarify

Line 224: Are the names of the P450’s annotated specific to T. yunnanensis? The authors are encouraged to submit these sequences to Dr. Nelson for their appropriate classification

Line 229: Please include the length of alignment

Lie 248: Rephrase the line to start with a word instead of a number or include the in the beginning of the sentence. Also, use transcripts and not genes throughout the manuscript

Line 261: A differential expression analysis using packages such as EdgeR, Deseq, or Voom are strongly encouraged to identify the differentially expressed transcripts between the different tissues of males and females.

 

 

 

 

 

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

The manuscript presents important scientific information that deserves to be published. I only suggest minor changes:

Line 3

Change “Tomicus yunnanensis” for “Tomicus yunnanensis Kirkendall and Faccoli, 2008 (Coleoptera, Scolytinae)”

Line 57

Change “Helicoverpa armigera” for “Helicoverpa armigera (Hübner, 1809) (Lepidoptera, Noctuidae)”

Line 64

Change “Dendroctonus armandi” for “Dendroctonus armandi Tsai and Li, 1959 (Coleoptera: Scolytinae)”

Line 71

Change Change “T. yunnanensis” for “Tomicus yunnanensis Kirkendall and Faccoli, 2008 (Coleoptera, Scolytinae)” - at the beginning of the sentence, present the scientific names in full.

Line 93

Include the number of specimens used in the study.

Lines 128-130

Change “Anoplophora glabripennis” for “Anoplophora glabripennis Motschulsky, 1854 (Coleoptera, Lamiinae)” - include this data for all scientific names.

Line 291

Change Change “T. yunnanensis” for “Tomicus yunnanensis”

Line 291

Y. pine means Yunnan pine? If yes, enter the non-abbreviated name.

Line 301

Change “Apis mellifera" for “Apis mellifera Linnaeus, 1758 (Hymenoptera: Apidae)”

Author Response

Please see the attachment.

Author Response File: Author Response.pdf