Characterization of Wnt Signaling Genes in Diaphorina citri , Asian Citrus Psyllid

Article activity feed

1. 

   GigaByte

   Sep 12, 2021

   This article is a preprint and has not been certified by peer review [what does this mean?].

   Chad Vosburg 1Indian River State College, Fort Pierce, FL 349812Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Chad VosburgMax Reynolds 1Indian River State College, Fort Pierce, FL 34981Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRita Noel 1Indian River State College, Fort Pierce, FL 34981Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTeresa Shippy 3KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KSFind this author on Google …

   This article is a preprint and has not been certified by peer review [what does this mean?].

   Chad Vosburg 1Indian River State College, Fort Pierce, FL 349812Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Chad VosburgMax Reynolds 1Indian River State College, Fort Pierce, FL 34981Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRita Noel 1Indian River State College, Fort Pierce, FL 34981Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTeresa Shippy 3KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KSFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Teresa ShippyPrashant S Hosmani 4Boyce Thompson Institute, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Prashant S HosmaniMirella Flores-Gonzalez 4Boyce Thompson Institute, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mirella Flores-GonzalezLukas A Mueller 4Boyce Thompson Institute, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lukas A MuellerWayne B Hunter 5USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Wayne B HunterSusan J Brown 3KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KSFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susan J BrownTom D’Elia 1Indian River State College, Fort Pierce, FL 34981Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tom D’EliaSurya Saha 4Boyce Thompson Institute, Ithaca, NY 148536Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Surya SahaFor correspondence: ss2489@cornell.edu

   This work has been peer reviewed in GigaByte (https://doi.org/10.46471/gigabyte.21), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

   Reviewer 1. Xingtan Zhang and Dongna Ma

   The manuscript by Vosburg et. al., systematically analyzed of the characteristics of the Wnt signaling genes in Diaphorina citri, and focusing on evolutionary history, expression patterns and potential functional. Finally, they also performed manual annotation of the Wnt signaling pathway. Indeed, this work would add important resource for the study of the evolutionary history of D. citri and Wnt signaling in this important hemipteran vector. The writing is acceptable. Even though, I still have some suggestion which may improve this manuscript.

   1. In the methods, the authors have indicated the process of identifying win genes, but the abstract describes it as Curation identification? I am confused whether this Wnt signaling genes in D. citri were identified by the author or whether the author just further analyzed it using the results already identified by others?
   2. The paper just did the identification of the win gene, evolutionary, and then the expression analysis using RNA-seq. It is recommended to also look at the chromosomal localization and mode of origin (e.g., tandem repeats)
   3. The Wnt signaling genes related to the hemipteran vector studied by the authors can be further verified by qPCR and then compared with the expression and function of other published insect-related genes for discussion.

   Major Revision.

   **Reviewer 2. Mary Ann Tuli ** Is the language of sufficient quality?
   Yes. The manuscript reads very well.

   Are all data available and do they match the descriptions in the paper?
   No. Additional Comments:

   1. Line 176. "High scoring MCOT models were then searched on the NCBI protein database...." We need the list Wnt pathway genes with high scoring MCOT models.

   2. Line 178. "The high scoring MCOT models that had promising NCBI search results were used to search the D. citri assembled genome." We need the list of high scoring MCOT models which had promising NCBI search results..

   3. Line 179. "Genome regions of high sequence identity to the query sequence were investigated within JBrowse" We need the list of models with high sequence identity with the assembled genome.

   4. Line 184. "MUSCLE multiple sequence alignments of the D. citri gene model sequences and orthologous sequences were created through MEGA7" We need the output of MUSCLE (FASTA). We need the files underlying the phylogenetic tree (newick).

   5. I note that MEGA7 has been used. I wonder why the newer release (MEGAX, March '21) was not used. Furthermore, the annotation protocol (dx.doi.org/10.17504/protocols.io.bniimcce) suggests using Mega7 or MegaX.

   Instructions on how to upload these files is given under "Any Additional Overall Comments to the Author".

   Are the data and metadata consistent with relevant minimum information or reporting standards?
   Yes. Nomenclature standards have been met. All cited INSDC accession numbers are publicly available.

   Is the data acquisition clear, complete and methodologically sound?
   Yes. Curation workflow used for community annotation is available via protocols.io , nonetheless the manuscript includes comprehensive summary which is appropriate.

   Is there sufficient detail in the methods and data-processing steps to allow reproduction? No. See "Are all data available and do they match the descriptions in the paper?" above. Once the additional files are made available I believe reproduction will be possible.

   Is there sufficient data validation and statistical analyses of data quality? Yes

   Is the validation suitable for this type of data? Yes

   Is there sufficient information for others to reuse this dataset or integrate it with other data? Yes

   Any Additional Overall Comments to the Author:
   Some of my comments/recommendations are pertinent to the other *D. citri *manuscripts currently under review.

   Minor Revision.

   Read the original source
2. 

   Version published to 10.1101/2020.09.21.306100v2 on bioRxiv

   Dec 13, 2020
3. 

   Version published to 10.1101/2020.09.21.306100v1 on bioRxiv

   Sep 22, 2020