Abstract: We have created an open access and public web portal with pathosystem-wide resources and bioinformatics tools for citrus, the vector Asian citrus psyllid (ACP) and multiple pathogens including Ca. Liberibacter asiaticus. This is the first example of a database to use the pathosystem as a more holistic framework to understand insect biology and disease transmission. The endeavor will connect and mine data sets generated by the community to study the citrus greening disease complex. We welcome submission of relevant data sets to enable sharing and allow the community to analyze data in an integrated system.
The portal contains a variety of tools for omics data. DiaphorinaCyc and CitrusCyc pathway databases can be used to analyze transcriptomics and proteomics results to identify pathways with differentially regulated genes. Psyllid Expression Network (PEN) contains profiles of ACP genes from multiple life stages, conditions and hosts. Citrus Expression Network (CEN) contains public expression data for citrus from NCBI. All tools like JBrowse, Biocyc, Blast, CEN and PEN connect to a central database containing gene models for citrus, ACP and multiple Liberibacter pathogens.
The portal also includes raw and annotated data from electrical penetration graph (EPG) recordings of ACP feeding on citrus and near relatives from published experiments. EPG datasets are extensive and only partially analyzed depending on particular questions of interest. Full datasets are released to encourage data mining and analysis by researchers interested in addressing questions related to ACP feeding behavior not addressed in our original publications.
The portal includes user-friendly manual curation tools to allow the research community to continuously improve this knowledge base as more experimental research is published. Bulk downloads are available for all genome and annotation datasets from the FTP site (ftp://ftp.citrusgreening.org). The portal can be accessed at https://citrusgreening.org/.
Non-technical summary: Citrusgreening.org is an open access and public web portal with information and omics resources for the host citrus, the vector psyllid and multiple pathogens including CLas. This data and resource hub is designed as a central repository for all data related to the citrusgreening disease complex. Scientists are encouraged to submit their data sets to the portal for sharing with the grower and research community.
Traditional Agroforestry System in India- Shifting Cultivation, Taungya, Home...
Citrusgreening.org: an Public Repository of Systems Biology Resources for the Huanglongbing (HLB) Disease Complex
1. www.citrusgreening.org
Citrusgreening.org: an Public Repository of
Systems Biology Resources for the
Huanglongbing (HLB) Disease Complex
Surya Saha
Boyce Thompson Institute, Ithaca, NY
ss2489@cornell.edu @SahaSurya
IRCHLB, March 14th, 2019
2. www.citrusgreening.org
Acknowledgements
Mueller Lab
Kansas State University
Sue Brown
USDA/ARS
Michelle (Cilia) Heck (Cornell Univ./BTI)
Wayne Hunter
Robert Shatters
Stephen L. Lapointe
John S. Ramsey
University of California, Davis
Carolyn Slupsky
Mirella Flores Prashant Hosmani Stephanie Hoyt
University of Florida
Lukasz Stelinski
Justin George
Cornell University
Denis Willett
Angela Kruse
Indian River State College
Tom D’elia
3. 500ng input DNA for Dovetail Chicago from single male psyllid
Duplicated contigs added to alternate assembly
Asian citrus psyllid(ACP) reference genome
v1.1 v2.0
REFERENCE
v3.0
REFERENCE
Number
of contigs
161,988 1,906 13 +
unplaced
Total
bases
485 Mb 498 Mb 475 Mb
Longest 1 Mb 4.2 Mb 50.3 Mb
Contig
N50
34.4 Kb 749 Kb 40Mb
Ns 19.3 Mb 4.5 Mb 12Mb
www.citrusgreening.org
Chicago and Hi-C
Poster: P9-101
5. Call for Data!!
www.citrusgreening.org
Resource Data types
Psyllid Expression Network (PEN) RNAseq, proteomics and metabolomics data
Citrus Expression Network (CEN) RNAseq, proteomics and metabolomics data
Metabolic pathway database
Lists of genes and pathways from publications. Curation of
predicted pathways
Manual gene curation
Structural and functional annotation. Meta-data from
publications for known or novel genes in citrus and the psyllid
Data portal
Electrical penetration graph, environmental, population genetics
and other data sets
Citrusgreening.org
6. Funding Available
Sequencing
• Illumina RNAseq
• Pacbio long read RNAseq (Iso-seq)
• Genomic sequencing
• Single cell RNA sequencing
Remote and On-site Training
• Annotation
• Web tools
Bioinformatics Analysis
• High performance computing
• Genome assembly
• Transcriptomics
• Population genetics
• Data analysis
Database support
• Web hosting
• New web tools
www.citrusgreening.org
7. www.citrusgreening.org
AgriVectors
Knowledge Base
Data Producers Data Consumers
Public
Repository
(remote)
Pathosystem
Repository
(local and remote)
Topic
Repository
(local and remote)
Researchers
Extension agents
Industry
USDA ARS / APHIS
CRISPR / RNAi genes
Microbiome
Geospatial disease data
Zebrachip
Citrusgreening
Pierce’s disease
Researchers
USDA ARS / APHIS / INRA
IPM product development
Outreach and extension
Educators
Secure portal
Patents
Commercial
AgriVectors
Portal
NCBI / EMBL / DDBJ
Ag Data Commons
i5k
8. www.citrusgreening.org
@Citrusgreening // @SahaSurya
Thank you!!
Posters: P10-175, P9-101, P10-120
Workshop (Thu, 6:30pm)
Citrusgreening.org and
Citrusgenomedb.org: What are
they and how to use them?
• Psyllid reference genome v3.0
• Manual curation of genes and pathways
• Metabolic pathway databases
• Psyllid Expression Network (PEN)
• Citrus Expression Network (CEN)