Citrusgreening.org –A systems biology resource for vector biologists

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”

mailto:[email protected]

www.citrusgreening.org

Got Data………. Now What?

• Deluge of data from different -omics technologies• Genomics

• Transcriptomics

• Proteomics

• Metabolomics

• Databases Excel

• Data integration

• Visualization


GMOD Tools


User Curation (Locus Editors)

Example from solgenomics.net


Genetic Maps

Example from solgenomics.net


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


Asian citrus psyllid (ACP)Diaphorina citri

CLasCandidatus Liberibacter asiaticus

Citrus spp.

The Biological Players

HostVector

Pathogen


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


Prashant Hosmani

Mirella Flores


Blast Databases


Gene Models, Repeats, RNAseq alignments, RNAseq coverage……..

Host, Vector and Pathogen references


Gene Models, Repeats, RNAseq alignments, RNAseq coverage ……..

Host, Vector and Pathogen references

Searchable index


Right-click to view gene details


CitrusCyc coming soon…..


DiaphorinaCyc

Cellular Overview of Diaphorina citri


DiaphorinaCyc

TCA cycle

Cellular Overview of Diaphorina citri


Upcoming Resources

• Locus pages

• ACP Expression Atlas• Transcriptomics• Proteomics• Metabolomics• MicroCT images

• Gene regulatory networks

Example from TEA


• Locus pages

• ACP Expression Atlas• Transcriptomics• Proteomics• Metabolomics• MicroCT images

• Gene regulatory networks

Upcoming Resources

Example from TEA


Outreach

• News

• Events

• Blog

• Publications


Acknowledgements

Cilia Lab:

Michelle Cilia

Annie Kruse

John Ramsey

Kansas State University:

Sue Brown

Citrusgreening.org –A systems biology resource for vector biologists

Science

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