citrusgreening.org –a systems biology resource for vector biologists
TRANSCRIPT
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Citrusgreening.org – A systems biology resource for vector biologists
Surya Saha
Boyce Thompson Institute for Plant Research
Mueller lab
[email protected] @SahaSurya
“Sequences to Disease Management”
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www.citrusgreening.org
Got Data………. Now What?
• Deluge of data from different -omics technologies• Genomics
• Transcriptomics
• Proteomics
• Metabolomics
• Databases Excel
• Data integration
• Visualization
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GMOD Tools
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www.citrusgreening.org
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User Curation (Locus Editors)
Example from solgenomics.net
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Genetic Maps
Example from solgenomics.net
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Citrus Greening: Huanglongbing• 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
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Asian citrus psyllid (ACP)Diaphorina citri
CLasCandidatus Liberibacter asiaticus
Citrus spp.
The Biological Players
HostVector
Pathogen
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Genomic Resources
Host• C. clementina (Clementine mandarin)
• 301.4 Mb with 1,398 scaffolds• 9 chromosomal pseudo-molecules (~21-51 Mb)
• C. sinensis (Sweet orange)• 319 Mb spread with 12,574 scaffolds• 236 scaffolds > 251 kb but no pseudomolecules
Vector• Diaphorina citri (Asian citrus psyllid)
• 485.7Mb assembly with 161,988 scaffolds• Scaffold N50 109.8kb
Pathogen• Candidatus Liberibacter asiaticus (CLas)
• 1.23Mb genome from a single psyllid
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Prashant Hosmani
Mirella Flores
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Blast Databases
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Blast Databases
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Gene Models, Repeats, RNAseq alignments, RNAseq coverage……..
Host, Vector and Pathogen references
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Gene Models, Repeats, RNAseq alignments, RNAseq coverage ……..
Host, Vector and Pathogen references
Searchable index
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Right-click to view gene details
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CitrusCyc coming soon…..
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DiaphorinaCyc
Cellular Overview of Diaphorina citri
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DiaphorinaCyc
Cellular Overview of Diaphorina citri
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DiaphorinaCyc
TCA cycle
Cellular Overview of Diaphorina citri
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DiaphorinaCyc
TCA cycle
Cellular Overview of Diaphorina citri
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Upcoming Resources
• Locus pages
• ACP Expression Atlas• Transcriptomics• Proteomics• Metabolomics• MicroCT images
• Gene regulatory networks
Example from TEA
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• Locus pages
• ACP Expression Atlas• Transcriptomics• Proteomics• Metabolomics• MicroCT images
• Gene regulatory networks
Upcoming Resources
Example from TEA
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Outreach
• News
• Events
• Blog
• Publications
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Acknowledgements
Cilia Lab:
Michelle Cilia
Annie Kruse
John Ramsey
Kansas State University:
Sue Brown