Diaci v3.0: Chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing

Authors: SHIPPY, TERESA - Kansas State University; HOSMANI, PRASHANT - Boyce Thompson Institute; FLORES-GONZALEZ, MIRELLA - Boyce Thompson Institute; MANN, MARINA - Cornell University; MILLER, SHERRY - Kansas State University; WEIRAUCH, MATTHEW - Cincinnati Children'S Research Hospital; VOSBERG, CHAD - Pennsylvania State University; MASSIMINO, CRISSY - Indian River State College; TANK, WILL - Kansas State University; DE OLIVEIRA, LUCAS - Indian River State College; Paris, Thomson; Shatters, Robert; Heck, Michelle; Hunter, Wayne

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/27/2024
Publication Date: 12/20/2024
Citation: Shippy TD, Hosmani PS, Flores-Gonzalez M, Mann M, Miller S, Weirauch MT, Vosberg C, Massimino C, Tank W, de Oliveira L, Chen C, Hoyt S, Adams R, Adkins S, Bailey ST, Chen X, Davis N, DeLaFlor Y, Espino M, Gervais K, Grace R, Harper D, Hasan DL, Hoang M, Holcomb R, Jernigan MR, Kemp M, Kennedy B, Kercher K, Klaessan S, Kruse A, Licata S, Lu A, Masse R, Mathew A, Michels S, Michels E, Neiman A, Norman S, Norus J, Ortiz Y, Panitz N, Paris T, Perentesis KMR, Perry M, Reynolds M, Sena MM, Tamayo B, Thate A, Vandervoort S, Ventura J, Weis N, Wise T, Shatters RG Jr, Heck M, Benoit JB, Hunter WB, Mueller LA, Brown SJ, D'Elia T, Saha S. Diaci v3.0: Chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing. Gigascience. 13:giae109. 2024. https://doi.org/10.1093/gigascience/giae109.
DOI: https://doi.org/10.1093/gigascience/giae109

Interpretive Summary: Researchers produced a significantly improved genome of the Asian citrus psyllid, that spreads the deadly bacterial pathogen of citrus trees. Thousands of genes were manually annotated which provided more accurate gene models for use by researchers to develop biopesticides to reduce psyllid populations and the data provided an excellent training opportunity for students from multiple institutions to learn gene identification. All genetic resources are available to the global research community at the website- CitrusGreening.org and at the National Center of Biotechnology Information, NCBI. The chromosomal- length genome assembly of the psyllid vector (Diaphorina citri) serves as a blueprint for the development of collaborative genomics projects for other medically and agriculturally significant insect vectors that spread important pathogens causing diseases.

Technical Abstract: Researchers produced a significantly improved genome, transcriptome, Diaci_v3.0, and the Official Gene Set, OGS_v3; of Diaphorina citri the psyllid vector of “Candidatus Liberibacter asiaticus” (CLas), the gram-negative bacterial pathogen associated with citrus greening disease. The 474-Mb genome has 13 chromosomal-length scaffolds. In total, 1,036 genes were manually curated as part of a community annotation project, composed primarily of undergraduate students. We also computationally identified a total of 1,015 putative transcription factors (TFs) and were able to infer motifs for 337 TFs (33%). In addition, we produced a genome-independent transcriptome and genomes for D. citri endosymbionts, Carsonella ruddii, Profftella armatura, and Wolbachia-Diaphorina. Control measures rely on pesticides with negative impacts on the environment, natural ecosystems, and human and animal health. In contrast, development of gene-targeting methods using these data, have the potential to specifically target the psyllid vector species to reduce pathogen transmission to citrus trees.