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Improved annotation of the insect vector of Citrus greening disease: Biocuration by a diverse genomics community

View ORCID ProfileSurya Saha, Prashant S Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa Shippy, Mirella Flores, Andrew Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Van Voorhis, Megan Dunlevy, David Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E Dixon, Andrew Cridge, Liliana Cano, Xialong Cao, Haobo Jiang, Nan Leng, Shannon Johnson, Brandi L Cantarel, Stephen Richardson, Adam English, Robert G Shatters, Chris Childers, Mei-Ju Chen, Wayne Hunter, Michelle Cilia, Lukas A Mueller, Monica Munoz-Torres, David Nelson, Monica F Poelchau, Joshua B Benoit, Helen Wiersma-Koch, Tom D’elia, Susan J Brown
doi: https://doi.org/10.1101/099168
Surya Saha
1Boyce Thompson Institute, Ithaca, NY 14853, USA
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  • ORCID record for Surya Saha
Prashant S Hosmani
1Boyce Thompson Institute, Ithaca, NY 14853, USA
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Krystal Villalobos-Ayala
2Indian River State College, Fort Pierce, FL 34981, USA
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Sherry Miller
3Kansas State University, Division of Biology, Manhattan, KS 66506, USA
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Teresa Shippy
3Kansas State University, Division of Biology, Manhattan, KS 66506, USA
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Mirella Flores
1Boyce Thompson Institute, Ithaca, NY 14853, USA
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Andrew Rosendale
4University of Cincinnati, Cincinnati, OH 45220, USA
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Chris Cordola
2Indian River State College, Fort Pierce, FL 34981, USA
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Tracey Bell
2Indian River State College, Fort Pierce, FL 34981, USA
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Hannah Mann
2Indian River State College, Fort Pierce, FL 34981, USA
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Gabe DeAvila
2Indian River State College, Fort Pierce, FL 34981, USA
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Daniel DeAvila
2Indian River State College, Fort Pierce, FL 34981, USA
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Zachary Moore
4University of Cincinnati, Cincinnati, OH 45220, USA
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Kyle Buller
4University of Cincinnati, Cincinnati, OH 45220, USA
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Kathryn Ciolkevich
4University of Cincinnati, Cincinnati, OH 45220, USA
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Samantha Nandyal
4University of Cincinnati, Cincinnati, OH 45220, USA
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Robert Mahoney
4University of Cincinnati, Cincinnati, OH 45220, USA
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Joshua Van Voorhis
4University of Cincinnati, Cincinnati, OH 45220, USA
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Megan Dunlevy
4University of Cincinnati, Cincinnati, OH 45220, USA
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David Farrow
4University of Cincinnati, Cincinnati, OH 45220, USA
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David Hunter
3Kansas State University, Division of Biology, Manhattan, KS 66506, USA
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Taylar Morgan
3Kansas State University, Division of Biology, Manhattan, KS 66506, USA
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Kayla Shore
3Kansas State University, Division of Biology, Manhattan, KS 66506, USA
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Victoria Guzman
3Kansas State University, Division of Biology, Manhattan, KS 66506, USA
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Allison Izsak
5Cornell University, Ithaca, NY 14853, USA
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Danielle E Dixon
1Boyce Thompson Institute, Ithaca, NY 14853, USA
6University of Puget Sound, Tacoma, WA 98416, USA
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Andrew Cridge
7University of Otago, North Dunedin, Dunedin 9016, New Zealand
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Liliana Cano
8University of Florida/ IFAS Indian River Research and Education Center, Plant Pathology, Ft. Pierce, FL 34945, USA
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Xialong Cao
14Oklahoma State University, Department of Biochemistry and Molecular Biology, Stillwater, OK 74074, USA
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Haobo Jiang
15Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK 74074, USA
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Nan Leng
13Illumina Inc., San Diego, CA 92122, USA
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Shannon Johnson
9Los Alamos National Laboratory, NM 87544, USA
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Brandi L Cantarel
10UT Southwestern Medical Center, Bioinformatics Core Facility, Department of Bioinformatics, Dallas, TX 75390, USA
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Stephen Richardson
11Baylor College of Medicine, i5K Arthropod Genomics, Houston, TX 77030, USA
12Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX 77030, USA
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Adam English
11Baylor College of Medicine, i5K Arthropod Genomics, Houston, TX 77030, USA
12Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX 77030, USA
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Robert G Shatters
18USDA ARS, U. S. Horticultural Research Laboratory, Ft. Pierce, FL 34945, USA
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Chris Childers
16USDA Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705, USA
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Mei-Ju Chen
17National Taiwan University, Graduate Institute of Biomedical Electronics and Bioinformatics, Taipei 10617, TW
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Wayne Hunter
18USDA ARS, U. S. Horticultural Research Laboratory, Ft. Pierce, FL 34945, USA
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Michelle Cilia
19USDA ARS, Emerging Pests and Pathogens Research Unit, Ithaca, NY 14853, USA
20Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Ithaca, NY 14853, USA
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Lukas A Mueller
1Boyce Thompson Institute, Ithaca, NY 14853, USA
21Cornell University, Plant Breeding and Genetics Section, School of Integrative Plant Science, Ithaca, NY 14853, USA
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Monica Munoz-Torres
22Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA 94720, USA
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David Nelson
23The University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, TN 38163, USA
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Monica F Poelchau
16USDA Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705, USA
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Joshua B Benoit
4University of Cincinnati, Cincinnati, OH 45220, USA
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Helen Wiersma-Koch
2Indian River State College, Fort Pierce, FL 34981, USA
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Tom D’elia
2Indian River State College, Fort Pierce, FL 34981, USA
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Susan J Brown
3Kansas State University, Division of Biology, Manhattan, KS 66506, USA
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ABSTRACT

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. All data are available on https://citrusgreening.org/.

Footnotes

  • ↵α Key personnel

  • ↵β Annotator

  • ↵– Genome Sequencing; Transcriptome; Principal Investigator

  • FUNDING All student annotators and post-docs were funded through USDA-NIFA grant 2015-7001623028. The genome sequencing was supported by grants from the NIH National Center for Research Resources (5P20RR016469). USDA-ARS, Ft. Pierce, FL and a grant from the Citrus Research Board, Inc. $12,000 (217 North Encina, P.O. Box 230, Visalia, CA. 93279)

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 04, 2017.
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Improved annotation of the insect vector of Citrus greening disease: Biocuration by a diverse genomics community
Surya Saha, Prashant S Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa Shippy, Mirella Flores, Andrew Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Van Voorhis, Megan Dunlevy, David Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E Dixon, Andrew Cridge, Liliana Cano, Xialong Cao, Haobo Jiang, Nan Leng, Shannon Johnson, Brandi L Cantarel, Stephen Richardson, Adam English, Robert G Shatters, Chris Childers, Mei-Ju Chen, Wayne Hunter, Michelle Cilia, Lukas A Mueller, Monica Munoz-Torres, David Nelson, Monica F Poelchau, Joshua B Benoit, Helen Wiersma-Koch, Tom D’elia, Susan J Brown
bioRxiv 099168; doi: https://doi.org/10.1101/099168
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Improved annotation of the insect vector of Citrus greening disease: Biocuration by a diverse genomics community
Surya Saha, Prashant S Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa Shippy, Mirella Flores, Andrew Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Van Voorhis, Megan Dunlevy, David Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E Dixon, Andrew Cridge, Liliana Cano, Xialong Cao, Haobo Jiang, Nan Leng, Shannon Johnson, Brandi L Cantarel, Stephen Richardson, Adam English, Robert G Shatters, Chris Childers, Mei-Ju Chen, Wayne Hunter, Michelle Cilia, Lukas A Mueller, Monica Munoz-Torres, David Nelson, Monica F Poelchau, Joshua B Benoit, Helen Wiersma-Koch, Tom D’elia, Susan J Brown
bioRxiv 099168; doi: https://doi.org/10.1101/099168

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