This document summarizes resources for studying the tritrophic disease complex of citrus greening. It describes a systems biology platform for visualizing omics data on genomics, transcriptomics, proteomics, and metabolomics. It outlines databases and tools developed for the citrus greening pathosystem, including genome browsers, biochemical pathway databases for the host, vector and pathogens, and an annotation editor. It details resources specific to the Asian citrus psyllid vector, such as a pathway database (DiaphorinaCyc), an expression atlas with omics data from various tissues, and a psyllid expression network. The goal is to utilize these system biology resources to better understand targets for interdicting the

1. Utilizing system biology resources to
decipher a tritrophic disease complex
Prashant Hosmani
Boyce Thompson Institute,
Ithaca, NY
psh65@cornell.edu
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2. Systems biology interactive data discovery platform
• Visualize complex biological data
Genomics
Transcriptomics
Proteomics
Metabolomics
• A platform for community to share
data
• Design can be replicated to any non-
model or invasive species
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https://www.ntnu.edu/biology/research/molecular-systems-biology

3. Citrus Greening: Huanglongbing
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Most significant disease of citrus worldwide
More than $4.5 billion in lost citrus production and more than 8,200 lost jobs (2006/07 to
2010/11)
Associated with gram negative bacterium Candidatus Liberibacter asiaticus (CLas)
Spread by insect vector, Diaphorina citri (Asian citrus psyllid, ACP)
Annie Kruse

4. Identification of targets for interdiction with Omics requires
better genomics resources
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Genome Annotation
Target for interdiction molecules
Pathway Databases
Regulatory Networks
…….

5. Citrusgreening.org
https://citrusgreening.org/
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Host, Vector and Pathogen(s)
 Blast Databases
 Genome browser – Jbrowse
 Biochemical pathway database
 Annotation Editor – Apollo
 Psyllid Expression Network (PEN)
 FTP site for download
Disease background
News, Publications, Links
Social Media

6. Biochemical pathway database - CitrusgreeningCyc’s
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Vector/Model
D. citri
D. melanogaster
Host
C. Clementina
C. sinensis
Bacteria
Ca. Liberibacter asiaticus, strain psy62
Ca. Liberibacter asiaticus, strain gxpsy
Ca. Liberibacter asiaticus, strain Ishi-1
Ca. Liberibacter americanus, strain Sao Paulo
Ca. Liberibacter solanacearum, strain CLso-ZC1
Ca. Liberibacter cresens, strain BT1
Wolbachia endosymbiont of D. melanogaster

7. Biochemical pathway database - DiaphorinaCyc
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Pathways: 185
Enzymes: 2855
Transport Reactions: 24
Proteins: 12548
Transporters: 77
Compounds: 1180

8. DiaphorinaCyc
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9. DiaphorinaCyc cellular overview with RNAseq
data
Cellular Overview of Diaphorina citri overlaid with RNAseq expression counts
Based on NCBI v100
Membrane proteins
Secretory
proteins
Membrane proteins
Kruse et al. (unpublished)
http://ptools.citrusgreening.org/overviewsWeb/celOv.shtml

10. Metabolic Pathway Database Construction
Genes
e.g. C sinensis, D citri
PathoLogic
Software
Reference Pathway
Database (MetaCyc)
Reactions
Pathways
Compounds
Gene products
Genes
Pathway/Genome
Database (CitrusCyc, DiaphorinaCyc)
Source: Peter Karp (SRI)
• Predicts metabolic pathways
• Predicts which genes code for missing enzymes in metabolic pathways
• Infers transport reactions from transporter names

11. Diaphorina citri Apollo annotation editor
Request access by contacting
https://citrusgreening.org/contact/form
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Genome assembly Diaci v1.91
Pacbio genome assembly scaffolded by Dovetail
chicago libraries
Users
• Indian River State College (IRSC)
• Kansas State University (KSU)
• University of Cincinnati (UC)
• Other expert annotators
More than 40 registered annotators

12. Psyllid Expression Network (PEN)
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Expression Atlas:
Various tissue and conditions for ACP
• Proteomics
• Transcriptomics
• Metabolomics
• MicroCT images
Proteomics - John Sawyer Ramsey (Heck lab)
Mirella Flores

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14. Psyllid Expression Network
Tissues
• Gut
• Salivary glands (Adults)
• Hemolymph (Adults)
• Nymph 4th/5th instar mixed
• Whole body (Adult)
• Blue fat body
• Bacteriome
• Egg
• Heads
• Male - Adults
• Female - Adults
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• RNAseq and proteomics
• Microtomography images and videos
• 3D view overlaid with expression data

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Surya Saha
Mirella Flores
Noe Fernandez
Lukas Mueller
Cornell University / BTI
Michelle (Cilia) Heck
Kansas State University
Susan Brown
Acknowledgements

16. Thank you!!
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