Annotation of segmentation pathway genes in the Asian citrus psyllid, Diaphorina citri

  1. Sherry Miller
  2. Teresa D. Shippy
  3. Prashant S. Hosmani
  4. Mirella Flores-Gonzalez
  5. Lukas A. Mueller
  6. Wayne B. Hunter
  7. Susan J. Brown
  8. Tom D’Elia
  9. Surya Saha

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Abstract

Insects have a segmented body plan that is established during embryogenesis when the anterior–posterior (A–P) axis is divided into repeated units by a cascade of gene expression. The cascade is initiated by protein gradients created by translation of maternally provided mRNAs, localized at the anterior and posterior poles of the embryo. Combinations of these proteins activate specific gap genes to divide the embryo into distinct regions along the anterior–posterior axis. Gap genes then activate pair-rule genes, which are usually expressed in parts of every other segment. The pair-rule genes, in turn, activate expression of segment polarity genes in a portion of each segment. The segmentation genes are generally conserved among insects, although there is considerable variation in how they are deployed. We annotated 25 segmentation gene homologs in the Asian citrus psyllid, Diaphorina citri. Most of the genes expected to be present in D. citri based on their phylogenetic distribution in other insects were identified and annotated. Two exceptions were eagle and invected, which are present in at least some hemipterans, but were not found in D. citri. Many of the segmentation pathway genes are likely to be essential for D. citri development, and thus they may be useful targets for gene-based pest control methods.

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    This article is a preprint and has not been certified by peer review [what does this mean?].

    Sherry Miller 1Division of Biology, Kansas State University, Manhattan, KS 665062Allen County Community College, Burlingame, KS 66413Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTeresa D. Shippy 1Division of Biology, Kansas State University, Manhattan, KS 66506Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Teresa D. ShippyPrashant S Hosmani 3Boyce 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 3Boyce Thompson Institute, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mirella Flores-GonzalezWayne B Hunter 4USDA-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 1Division of Biology, Kansas State University, Manhattan, KS 66506Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susan J BrownTom D’elia 5Indian 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 3Boyce 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.26), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

    **Reviewer 1. Hailin Liu **It seems there are no very sound biological values in this manuscript, and more validation or comparative study are suggested to mine more meaningful conclusions.

    **Reviewer 2. Mary Ann Tuli ** Please add additional comments on language quality to clarify if needed : The manuscript reads very well.

    Are all data available and do they match the descriptions in the paper?
    No. Additional Comments: 1) Line 206. "Multiple alignments were performed with MUSCLE or MEGA7 " (figure 1). We need the output of MUSCLE (FASTA). We need the output of MEGA7 (FASTA)

    1. 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.

    2. Line 207. "phylogenetic analysis was done in MEGA7 or MEGA X" (figure 2). We need the files underlying the phylogenetic tree (newick) (figure 2).

    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.

  2. Version published to 10.46471/gigabyte.26
  3. Version published to 10.1101/2020.12.24.424320v1 on bioRxiv