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

Autor:	Shippy TD; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., Hosmani PS; Boyce Thompson Institute, Ithaca, NY 14853, USA.; Syngenta Seeds Inc, 9 Davis Dr, Research Triangle Park, NC 27709, USA., Flores-Gonzalez M; Boyce Thompson Institute, Ithaca, NY 14853, USA., Mann M; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA., Miller S; Division of Biology, Kansas State University, Manhattan, KS 66506, USA.; Allen County Community College, Burlingame, KS 66413, USA., Weirauch MT; The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 15012, USA., Vosberg C; 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., Massimino C; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Tank W; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., de Oliveira L; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Chen C; Boyce Thompson Institute, Ithaca, NY 14853, USA., Hoyt S; Boyce Thompson Institute, Ithaca, NY 14853, USA., Adams R; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Adkins S; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Bailey ST; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Chen X; The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 15012, USA., Davis N; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., DeLaFlor Y; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Espino M; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Gervais K; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Grace R; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Harper D; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Hasan DL; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Hoang M; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Holcomb R; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Jernigan MR; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Kemp M; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Kennedy B; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., Kercher K; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Klaessan S; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Kruse A; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA., Licata S; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Lu A; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., Masse R; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Mathew A; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Michels S; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Michels E; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Neiman A; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Norman S; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Norus J; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Ortiz Y; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Panitz N; Boyce Thompson Institute, Ithaca, NY 14853, USA., Paris T; 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., Perentesis KMR; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Perry M; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Reynolds M; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Sena MM; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Tamayo B; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Thate A; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., Vandervoort S; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., Ventura J; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Weis N; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., Wise T; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Shatters RG Jr; US Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA., Heck M; 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., Benoit JB; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA., Hunter WB; US Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA., Mueller LA; Boyce Thompson Institute, Ithaca, NY 14853, USA., Brown SJ; Division of Biology, Kansas State University, Manhattan, KS 66506, USA., D'Elia T; Department of Biological Sciences, Indian River State College, Fort Pierce, FL 34981, USA., Saha S; Boyce Thompson Institute, Ithaca, NY 14853, USA.
Jazyk:	angličtina
Zdroj:	GigaScience [Gigascience] 2024 Jan 02; Vol. 13.
DOI:	10.1093/gigascience/giae109
Abstrakt:	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. (© The Author(s) 2024. Published by Oxford University Press GigaScience.)
Databáze:	MEDLINE
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