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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, 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 2024; 13:giae109. [PMID: 39704701 PMCID: PMC11659978 DOI: 10.1093/gigascience/giae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 07/25/2023] [Accepted: 11/27/2024] [Indexed: 12/21/2024] Open
Abstract
BACKGROUND Diaphorina citri is an insect vector of "Candidatus Liberibacter asiaticus" (CLas), the gram-negative bacterial pathogen associated with citrus greening disease. Control measures rely on pesticides with negative impacts on the environment, natural ecosystems, and human and animal health. In contrast, gene-targeting methods have the potential to specifically target the vector species and/or reduce pathogen transmission. RESULTS To improve the genomic resources needed for targeted pest control, we assembled a D. citri genome based on PacBio long reads followed by proximity ligation-based scaffolding. 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. CONCLUSIONS Manual annotation provided more accurate gene models for use by researchers and provided an excellent training opportunity for students from multiple institutions. All resources are available on CitrusGreening.org and NCBI. The chromosomal-length D. citri genome assembly serves as a blueprint for the development of collaborative genomics projects for other medically and agriculturally significant insect vectors.
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Affiliation(s)
- Teresa D Shippy
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Prashant S Hosmani
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Syngenta Seeds Inc, 9 Davis Dr, Research Triangle Park, NC 27709, USA
| | | | - Marina Mann
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Sherry Miller
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
- Allen County Community College, Burlingame, KS 66413, USA
| | - Matthew T Weirauch
- The Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 15012, USA
| | - Chad Vosberg
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Crissy Massimino
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Will Tank
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Lucas de Oliveira
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Chang Chen
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | | | - Rebekah Adams
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Samuel Adkins
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Xiaoting Chen
- The Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 15012, USA
| | - Nina Davis
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Yesmarie DeLaFlor
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Michelle Espino
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Kylie Gervais
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Rebecca Grace
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Douglas Harper
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Denisse L Hasan
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Maria Hoang
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Rachel Holcomb
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Margaryta R Jernigan
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Melissa Kemp
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Bailey Kennedy
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kyle Kercher
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Stefan Klaessan
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Angela Kruse
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Sophia Licata
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Andrea Lu
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ron Masse
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Anuja Mathew
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Sarah Michels
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Elizabeth Michels
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Alan Neiman
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Seantel Norman
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jordan Norus
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Yasmin Ortiz
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Thomson Paris
- US Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA
- Entomology and Nematology Department, North Florida Research and Education Center, University of Florida, Fort Pierce, FL 32351, USA
| | - Kitty M R Perentesis
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Michael Perry
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Max Reynolds
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Madison M Sena
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Blessy Tamayo
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Amanda Thate
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Sara Vandervoort
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Jessica Ventura
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Nicholas Weis
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Tanner Wise
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Robert G Shatters
- US Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, USDA-ARS, Ithaca, NY 14850, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Wayne B Hunter
- US Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA
| | | | - Susan J Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Tom D'Elia
- Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA
| | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY 14853, USA
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Martins da Silva R, de Oliveira Daumas Filho CR, Calixto C, Nascimento da Silva J, Lopes C, da Silva Vaz I, Logullo C. PEPCK and glucose metabolism homeostasis in arthropods. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 160:103986. [PMID: 37454751 DOI: 10.1016/j.ibmb.2023.103986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
The fat body is responsible for a variety of functions related to energy metabolism in arthropods, by controlling the processes of de novo glucose production (gluconeogenesis) and glycogen metabolism. The rate-limiting factor of gluconeogenesis is the enzyme phosphoenolpyruvate carboxykinase (PEPCK), generally considered to be the first committed step in this pathway. Although the study of PEPCK and gluconeogenesis has been for decades restricted to mammalian models, especially focusing on muscle and liver tissue, current research has demonstrated particularities about the regulation of this enzyme in arthropods, and described new functions. This review will focus on arthropod PEPCK, discuss different aspects to PEPCK regulation and function, its general role in the regulation of gluconeogenesis and other pathways. The text also presents our views on potentially important new directions for research involving this enzyme in a variety of metabolic adaptations (e.g. diapause), discussing enzyme isoforms, roles during arthropod embryogenesis, as well as involvement in vector-pathogen interactions, contributing to a better understanding of insect vectors of diseases and their control.
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Affiliation(s)
- Renato Martins da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT, Rio de Janeiro, RJ, Brazil
| | - Carlos Renato de Oliveira Daumas Filho
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT, Rio de Janeiro, RJ, Brazil
| | - Christiano Calixto
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT, Rio de Janeiro, RJ, Brazil
| | - Jhenifer Nascimento da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT, Rio de Janeiro, RJ, Brazil
| | - Cintia Lopes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT, Rio de Janeiro, RJ, Brazil
| | - Itabajara da Silva Vaz
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT, Rio de Janeiro, RJ, Brazil; Centro de Biotecnologia and Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Carlos Logullo
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT, Rio de Janeiro, RJ, Brazil.
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