Citrusgreening.org – A systems biology resource for vector biologists

Surya Saha

Boyce Thompson Institute for Plant Research

Mueller lab

ss2489@cornell.edu @SahaSurya

“Sequences to Disease Management”

www.citrusgreening.org

Got Data………. Now What?

• Deluge of data from different -omics technologies• Genomics

• Transcriptomics

• Proteomics

• Metabolomics

• Databases Excel

• Data integration

• Visualization

www.citrusgreening.org

GMOD Tools

www.citrusgreening.org

www.citrusgreening.org

User Curation (Locus Editors)

Example from solgenomics.net

www.citrusgreening.org

Genetic Maps

Example from solgenomics.net

www.citrusgreening.org

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

www.citrusgreening.org

Asian citrus psyllid (ACP)Diaphorina citri

CLasCandidatus Liberibacter asiaticus

Citrus spp.

The Biological Players

HostVector

Pathogen

www.citrusgreening.org

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

www.citrusgreening.org

Prashant Hosmani

Mirella Flores

www.citrusgreening.org

Blast Databases

www.citrusgreening.org

Blast Databases

www.citrusgreening.org

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

Host, Vector and Pathogen references

www.citrusgreening.org

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

Host, Vector and Pathogen references

Searchable index

www.citrusgreening.org

Right-click to view gene details

www.citrusgreening.org

CitrusCyc coming soon…..

www.citrusgreening.org

DiaphorinaCyc

Cellular Overview of Diaphorina citri

www.citrusgreening.org

DiaphorinaCyc

Cellular Overview of Diaphorina citri

www.citrusgreening.org

DiaphorinaCyc

TCA cycle

Cellular Overview of Diaphorina citri

www.citrusgreening.org

DiaphorinaCyc

TCA cycle

Cellular Overview of Diaphorina citri

www.citrusgreening.org

Upcoming Resources

• Locus pages

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

• Gene regulatory networks

Example from TEA

www.citrusgreening.org

• Locus pages

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

• Gene regulatory networks

Upcoming Resources

Example from TEA

www.citrusgreening.org

Outreach

• News

• Events

• Blog

• Publications

www.citrusgreening.org

Acknowledgements

Cilia Lab:

Michelle Cilia

Annie Kruse

John Ramsey

Kansas State University:

Sue Brown