Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features

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

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Abstract

Hox genes and their cofactors are essential developmental genes that specify regional identity in animals, including insects. A particularly interesting feature of Hox genes is their conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. Among insects, breaks in the cluster have been reported in a few species, but these seem to be the exception rather than the rule. We have annotated the ten Hox genes of the Asian citrus psyllid, Diaphorina citri, and determined that there is a split in its Hox cluster between the Deformed and Sex combs reduced genes. This is the first time a break at this position has been observed in an insect Hox cluster. We have also annotated the D. citri orthologs of the Hox cofactor genes homothorax, PKNOX and extradenticle. Interestingly, we found an additional copy of extradenticle in D. citri that appears to be a retrogene. Expression data and sequence conservation suggest that the extradenticle retrogene may have retained the original extradenticle function and allowed the parental extradenticle gene to diverge.

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  1. GigaByte

    Now published in Gigabyte doi: 10.46471/gigabyte.49

    Teresa Shippy 1 KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Teresa ShippyPrashant S Hosmani 2 Boyce Thompson Institute, Ithaca, NY 14853; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Prashant S HosmaniMirella Flores-Gonzalez 2 Boyce Thompson Institute, Ithaca, NY 14853; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mirella Flores-GonzalezLukas A Mueller 2 Boyce Thompson Institute, Ithaca, NY 14853; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lukas A MuellerWayne B Hunter 3 USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Wayne B HunterSusan J Brown 1 KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susan J BrownTom DeliaFIXX 4 Indian River State College, Fort Pierce, FL 34981; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tom DeliaFIXXSurya Saha 5 Boyce Thompson Institute Find 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 published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.49), and has published the reviews under the same license. These are as follows.

    **Reviewer 1. Hailin Liu **

    Is the data acquisition clear, complete and methodologically sound? No.

    Additional Comments:

    Minor revision please:

    1. This manuscript needs to be reorganized, as the methods, results and discussion were somewhat mixed.
    2. Line 125, were these data newly got? How much data you used should also be presented.
    3. How do you make sure that the hox genes you find were complete or exact? Was there any validation?

    Recommendation: Minor Revision

    **Reviewer 2. Mary Ann Tuli **

    Are all data available and do they match the descriptions in the paper?

    Yes. he author states, "Reciprocal BLAST was used to confirm orthologs for all D. citri genes", and has explained (through the pre-review process) that these were performed manually on the NCBI website over a period of months by different authors and thus cannot be easily reproduced. I think it could be made more clear that this is in line with manual curation and the accession numbers are all provided in the paper.

    Is there sufficient detail in the methods and data-processing steps to allow reproduction?

    Yes. See above comment regarding reciprocal BLAST.

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

    Yes. It does meet reuse criteria, but will be more reusable once the data is available from the Citrus Greening website.

    Recommendation: Minor Revision

  2. Version 1 published on bioRxiv