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Title: Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Journal Article · · Database
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  1. Boyce Thompson Inst. for Plant Research, Ithaca, NY (United States)
  2. Indian River State College, Fort Pierce, FL (United States)
  3. Kansas State Univ., Manhattan, KS (United States). Division of Biology
  4. Univ. of Cincinnati, OH (United States)
  5. Cornell Univ., Ithaca, NY (United States)
  6. Boyce Thompson Inst. for Plant Research, Ithaca, NY (United States); Univ. Puget Sound, Tacoma, WA (United States)
  7. Univ. of Otago, North Dunedin (New Zealand)
  8. Univ. of Florida, Ft. Pierce, FL (United States). Plant Pathology and IFAS Indian River Research and Education Center (IRREC)
  9. Baylor College of Medicine, Houston, TX (United States). i5K Arthropod Genomics
  10. Baylor College of Medicine, Houston, TX (United States). Human Genome Sequencing Center
  11. Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Bioinformatics
  12. Oklahoma State Univ., Stillwater, OK (United States). Dept. of Biochemistry and Molecular Biology
  13. Oklahoma State Univ., Stillwater, OK (United States). Dept. of Entomology and Plant Pathology
  14. Illumina Inc., San Diego, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  15. US Dept. of Agriculture (USDA), Fort Pierce, FL (United States). Agricultural Research Service, Horticultural Research Lab.
  16. US Dept. of Agriculture (USDA), Beltsville, MD (United States). Agricultural Research Service, National Agricultural Library
  17. National Taiwan Univ., Taipei (Taiwan). Graduate Inst. of Biomedical Electronics and Bioinformatics
  18. US Dept. of Agriculture (USDA), Ithaca, NY (United States). Agricultural Research Service, Emerging Pests and Pathogens Research Unit; Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section
  19. Boyce Thompson Inst. for Plant Research, Ithaca, NY (United States); Cornell Univ., Ithaca, NY (United States) School of Integrative Plant Science, Plant Breeding and Genetics Section
  20. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
  21. Univ. of Tennessee Health Science Center, Memphis, TN, (United States). Dept. of Microbiology, Immunology and Biochemistry
+ Show Author Affiliations

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE; USDA; National Institute of Food and Agriculture (NIFA); National Institutes of Health (NIH); National Center for Research Resources (NCRR); Citrus Research Board, Inc.; Agricultural Research Service (ARS)
Grant/Contract Number:
89233218CNA000001; 2015-70016-23028; 5P20RR016469
OSTI ID:
1625308
Journal Information:
Database, Vol. 2017; ISSN 1758-0463
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 14 works
Citation information provided by
Web of Science

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Cited By (10)

Comparative genomics analysis of triatomines reveals common first line and inducible immunity-related genes and the absence of Imd canonical components among hemimetabolous arthropods journal January 2018
A Small Wolbachia Protein Directly Represses Phage Lytic Cycle Genes in “ Candidatus Liberibacter asiaticus” within Psyllids journal June 2017
Insect Transmission of Plant Pathogens: a Systems Biology Perspective journal March 2018
Double triage to identify poorly annotated genes in maize: The missing link in community curation journal October 2019
A quick guide for student-driven community genome annotation journal April 2019
Lessons from One Fastidious Bacterium to Another: What Can We Learn about Liberibacter Species from Xylella fastidiosa journal September 2019
A quick guide for student-driven community genome annotation text January 2018
By land, air, and sea: hemipteran diversity through the genomic lens journal February 2018
Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut journal June 2017
Rhodnius prolixus: Identification of missing components of the IMD immune signaling pathway and functional characterization of its role in eliminating bacteria journal April 2019

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