Genomic identification, annotation, and comparative analysis of Vacuolar-type ATP synthase subunits in Diaphorina citri

  1. Rebecca Grace
  2. Crissy Massimino
  3. Teresa D. Shippy
  4. Will Tank
  5. Prashant S. Hosmani
  6. Mirella Flores-Gonzalez
  7. Lukas A. Mueller
  8. Wayne B. Hunter
  9. Joshua B. Benoit
  10. Susan J. Brown
  11. Tom D’Elia
  12. Surya Saha
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Abstract

Detailed annotation and comparative analysis were performed on the Asian citrus psyllid (ACP), Diaphorina citri , vacuolar-type ATP synthase (V-ATPase) to support the biological understanding and development of novel therapeutics to manage psyllid vectors. D. citri is a hemipteran insect that vectors the causative agent, the bacteria Candidatus Liberibacter asiaticus ( C Las), of the citrus greening disease, Huanglongbing (HLB). Millions of citrus trees have been destroyed by citrus greening and every grove in Florida has been directly impacted. In eukaryotic organisms, V-ATPase is an abundant heterodimeric enzyme that serves the cell with essential compartment acidification through the active processes that transport protons across the membrane. Manual curation was completed on 15 putative V-ATPase genes in the D. citri genome. Comparative genomic analysis reveals that the D. citri V-ATPase subunits share domains and motifs with other insects, including the V-ATPase-A superfamily domain from the V-ATPase catalytic subunit A, which shares a 92% identity with Acyrthosiphon pisum . Phylogenetic analysis separates D. citri V-ATPase subunits into expected clades with orthologous sequences. Based on the results of annotation and comparative genomic analysis, RNAi therapies targeting D. citri V-ATPase genes, which have been successfully utilized in related hemipterans, are being pursued. Annotation of the D. citri genome is a critical step towards the development of directed-pest management that will lead to the reduced spread of the pathogens causing HLB throughout the citrus industry.

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  1. GigaByte

    Abstract

    A version of this preprint has been published in the journal GigaByte under a CC-BY 4.0 license (see paper), and is also part of the Asian citrus psyllid community annotation series of papers that can be viewed here: https://doi.org/10.46471/GIGABYTE_SERIES_0001

    **Reviewer 1. Alex Arp ** In “Genomic identification, annotation, and comparative analysis of Vacuolar-type ATP synthase subunits in Diaphorina citri” the authors did just that. The paper is well written, direct, and easy to follow. The reasoning of annotating these genes is clearly defined; that they are possible targets for RNAi based control for Diaphorina citri, an economically important pest of citrus. The annotation of the genes utilized genomic and transcriptomic databases and the gene expression profiles used existing datasets. Figures and Tables are clear and the phylogenetic trees give sufficient supporting evidence that the annotations are correct. Overall is a good manuscript and needs no major revision for publication.

    Additional Comments: On Page 18 what is meant by "new protein" in "It is a relatively new protein critically associated with the assembly of a certain cell type V-ATPase and is still being studied"?

    **Reviewer 2. Mary Ann Tuli ** Are all data available and do they match the descriptions in the paper?

    Yes. As with the other manuscripts, OGS v3 is mentioned, but this is not get available from the CGEN. The requesting data underlying table and figures has been uploaded.

    Any Additional Overall Comments to the Author This manuscript is a comprehensive description of the manual curation of the V-ATPase genes, with clear aims and methodology.

    Recommendation: Accept

  2. Version 1 published on bioRxiv